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@ -16,10 +16,10 @@ in with self; {
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ADaCGH2 = derive2 { name="ADaCGH2"; version="2.36.0"; sha256="0awjxl2lwyh7hkjsx1zqsvrh649s9zn89za1iv8yd9l48ch2zfs5"; depends=[aCGH bit cluster DNAcopy ff GLAD snapCGH tilingArray waveslim]; };
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AGDEX = derive2 { name="AGDEX"; version="1.44.0"; sha256="0c44fw5ajdjc13409rn3lsv0jhlqa2qcak9b1k8hpig486xxzsr9"; depends=[Biobase GSEABase]; };
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AIMS = derive2 { name="AIMS"; version="1.28.0"; sha256="1z7yzaizyzcv556w8880603nd947k0d6raadjm42mdl66mma0cdx"; depends=[Biobase e1071]; };
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ALDEx2 = derive2 { name="ALDEx2"; version="1.28.0"; sha256="1dx0ipj0vrickya4742zacdgrg9a0i9b4j4cxhld2bk77pmdvx38"; depends=[BiocParallel GenomicRanges IRanges multtest Rfast S4Vectors SummarizedExperiment zCompositions]; };
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ALDEx2 = derive2 { name="ALDEx2"; version="1.28.1"; sha256="0xppx52sllbz4pli174422i4kkf37v0yl844088nbj3j9r6pfbj9"; depends=[BiocParallel GenomicRanges IRanges multtest Rfast S4Vectors SummarizedExperiment zCompositions]; };
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AMARETTO = derive2 { name="AMARETTO"; version="1.12.0"; sha256="111dk19b9910icksyr592cvhc5gwvgknr5q4887j9yxbajd7hcmx"; depends=[BiocFileCache callr circlize ComplexHeatmap curatedTCGAData doParallel dplyr DT foreach ggplot2 glmnet gridExtra httr impute knitr limma Matrix matrixStats MultiAssayExperiment Rcpp readr reshape2 rmarkdown tibble]; };
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AMOUNTAIN = derive2 { name="AMOUNTAIN"; version="1.22.0"; sha256="0vdfabsrisdd7qq28f5ivd0v8zz49szqn677i5lhwnlaix220c54"; depends=[]; };
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ANCOMBC = derive2 { name="ANCOMBC"; version="1.6.0"; sha256="18yzi361qw2731s8bi23q7mjyk32gm6pmc2vb1kwqs97yipz5wrh"; depends=[MASS microbiome nloptr phyloseq Rdpack]; };
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ANCOMBC = derive2 { name="ANCOMBC"; version="1.6.1"; sha256="1p9yryv85qk7m3hbflmpdffd3azpsifcw54x1rp8sb67yjmq3whq"; depends=[DescTools doParallel doRNG dplyr energy foreach Hmisc magrittr MASS microbiome nlme nloptr phyloseq Rdpack rlang tibble tidyr]; };
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ANF = derive2 { name="ANF"; version="1.18.0"; sha256="1fa2pbdapymrpz01ws0m2fbzf11d723x6rbsys29v06is57f5lpj"; depends=[Biobase igraph MASS RColorBrewer survival]; };
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APAlyzer = derive2 { name="APAlyzer"; version="1.10.0"; sha256="1xixj6ck1akwc01gv7xsgnnflrkhflsrpq2cbxh5s7z6xj0f8k00"; depends=[DESeq2 dplyr GenomicAlignments GenomicFeatures GenomicRanges ggplot2 ggrepel HybridMTest repmis Rsamtools Rsubread rtracklayer SummarizedExperiment tidyr VariantAnnotation]; };
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APL = derive2 { name="APL"; version="1.0.0"; sha256="1089klbirrnm99xw02bd0hfzqnhcq5fas9hw1l52x191j7b0363r"; depends=[ggplot2 ggrepel magrittr org_Hs_eg_db org_Mm_eg_db plotly reticulate rlang Seurat SingleCellExperiment SummarizedExperiment topGO viridisLite]; };
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@ -31,10 +31,10 @@ in with self; {
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ASSET = derive2 { name="ASSET"; version="2.14.0"; sha256="029acl5k9d4hnvy3jia9cr4rk6w31zn8b5s79i6lazq1cp236hbg"; depends=[MASS msm rmeta]; };
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ASSIGN = derive2 { name="ASSIGN"; version="1.32.0"; sha256="1f1lqip58cvf85nmq8mj7phlk0plcfv1h5ihc0cf2h5y7n4wrm9n"; depends=[ggplot2 gplots msm Rlab sva yaml]; };
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ASURAT = derive2 { name="ASURAT"; version="1.0.0"; sha256="160wvlvyc5dddjngmd21s1av292f6nvjkabag9iz8dipivicyi23"; depends=[circlize cluster ComplexHeatmap plot3D Rcpp S4Vectors SingleCellExperiment SummarizedExperiment]; };
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ASpediaFI = derive2 { name="ASpediaFI"; version="1.10.0"; sha256="1wn7iwaj92j1qvfp4l93ir4dawd1yczff3qyhh886qw2jcbf0b99"; depends=[BiocParallel biomaRt dplyr DRaWR e1071 fgsea GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 Gviz igraph IRanges IVAS limma Matrix mGSZ reshape2 ROCR Rsamtools rtracklayer S4Vectors scales SummarizedExperiment]; };
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ASpediaFI = derive2 { name="ASpediaFI"; version="1.10.0"; sha256="1wn7iwaj92j1qvfp4l93ir4dawd1yczff3qyhh886qw2jcbf0b99"; depends=[BiocParallel biomaRt dplyr DRaWR e1071 fgsea GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 Gviz igraph IRanges IVAS limma Matrix reshape2 ROCR Rsamtools rtracklayer S4Vectors scales SummarizedExperiment]; };
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ASpli = derive2 { name="ASpli"; version="2.6.0"; sha256="1frlcwa8m4imfx6ncav8r8yskyaf4ibha177mfnp9y84w6mphynz"; depends=[AnnotationDbi BiocGenerics BiocStyle data_table DT edgeR GenomicAlignments GenomicFeatures GenomicRanges Gviz htmltools igraph IRanges limma MASS pbmcapply Rsamtools S4Vectors tidyr UpSetR]; };
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ATACseqQC = derive2 { name="ATACseqQC"; version="1.20.2"; sha256="0jj7n0mcj0gciw0ksazlksgmwzp51a40pwqhf0c7la0cc4bnrkqp"; depends=[BiocGenerics Biostrings BSgenome ChIPpeakAnno edgeR GenomeInfoDb GenomicAlignments GenomicRanges GenomicScores IRanges KernSmooth limma motifStack preseqR randomForest Rsamtools rtracklayer S4Vectors]; };
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AUCell = derive2 { name="AUCell"; version="1.18.0"; sha256="11dh5nv3fljy9qmm1pnhqdsl20k2y0n82pqrrijf3ymj37y4bdgz"; depends=[BiocGenerics data_table DelayedArray DelayedMatrixStats GSEABase mixtools R_utils shiny SummarizedExperiment]; };
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AUCell = derive2 { name="AUCell"; version="1.18.1"; sha256="17wr7dycll0l1gax4w268qw7is163bs51rj6p1qnx1dgc9ibnsgr"; depends=[BiocGenerics data_table DelayedArray DelayedMatrixStats GSEABase mixtools R_utils shiny SummarizedExperiment]; };
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AWFisher = derive2 { name="AWFisher"; version="1.10.0"; sha256="050k7w0azsl7rqx2pxgccihzc2q8pmh6fyy4gib2d42sdyijr2n1"; depends=[edgeR limma]; };
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AffiXcan = derive2 { name="AffiXcan"; version="1.14.0"; sha256="0wj9shzmlxpksbxny571xzfcmmqqzjlk1vq4mx1is2r6ma7jkblq"; depends=[BiocParallel crayon MultiAssayExperiment SummarizedExperiment]; };
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AffyCompatible = derive2 { name="AffyCompatible"; version="1.56.0"; sha256="0x3lj1jgqq67389rzfklah5p878ns9b4fpdpz455m2gq9sk7qsda"; depends=[Biostrings RCurl XML]; };
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@ -43,7 +43,7 @@ in with self; {
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AllelicImbalance = derive2 { name="AllelicImbalance"; version="1.34.0"; sha256="0w4xd0xzkwx7bbhrgqligpahlhg85rginknx520z891r8v0bim2z"; depends=[AnnotationDbi BiocGenerics Biostrings BSgenome GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges gridExtra Gviz IRanges lattice latticeExtra nlme Rsamtools S4Vectors seqinr SummarizedExperiment VariantAnnotation]; };
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AlphaBeta = derive2 { name="AlphaBeta"; version="1.10.0"; sha256="1ikdrigma02gnl6ggrc89bjsiqmd7knpb9kw7nqyrdnv3qjd9iag"; depends=[BiocParallel data_table dplyr expm ggplot2 gtools igraph optimx plotly stringr]; };
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AlpsNMR = derive2 { name="AlpsNMR"; version="3.6.0"; sha256="0gmzabwidvh1ja8821sc2whn8nhw6g26694f35x1193kpr858qih"; depends=[baseline BiocParallel dplyr fs future ggplot2 glue htmltools magrittr matrixStats mixOmics pcaPP purrr readxl reshape2 rlang rmarkdown signal speaq stringr tibble tidyr vctrs]; };
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AnVIL = derive2 { name="AnVIL"; version="1.8.0"; sha256="13f9jivc53p5hixmpwiqcqdns0yq3mskvlzc40g0ckz7v52jy63b"; depends=[BiocManager dplyr futile_logger httr jsonlite rapiclient rlang tibble tidyr tidyselect]; };
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AnVIL = derive2 { name="AnVIL"; version="1.8.3"; sha256="10wd56brz0y0zyi6qd9nx11s04a6h56yzdnfd2m28r8y6x9dxhg4"; depends=[BiocManager dplyr futile_logger httr jsonlite rapiclient rlang tibble tidyr tidyselect]; };
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AnVILBilling = derive2 { name="AnVILBilling"; version="1.6.0"; sha256="08bc1lsjkgs0hmrfi2fbk5swbi5ckgrv4vhsfkqqywfpnkq9k436"; depends=[bigrquery DBI dplyr DT ggplot2 lubridate magrittr plotly shiny shinytoastr]; };
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AnVILPublish = derive2 { name="AnVILPublish"; version="1.6.0"; sha256="1iwvm60lricpsf4nr99wxhni0lwaa4z8aibr7lwj9gdwf2y43c9x"; depends=[AnVIL httr jsonlite readr rmarkdown whisker yaml]; };
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Anaquin = derive2 { name="Anaquin"; version="2.20.0"; sha256="1jgpnls2djl1yzvnk64qc83mljmlci7wflwkza3wr0sv6r47b0dd"; depends=[DESeq2 ggplot2 knitr locfit plyr qvalue ROCR]; };
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@ -89,8 +89,8 @@ in with self; {
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BayesKnockdown = derive2 { name="BayesKnockdown"; version="1.22.0"; sha256="122vg0lvs3fkgwcvn259rk0m1vaz19pdfvhsj5m1hd3d2h44pv65"; depends=[Biobase]; };
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BayesSpace = derive2 { name="BayesSpace"; version="1.6.0"; sha256="0086fw2chymjwxwgzax6lky84kaa34900ca2p90pbjqx14b161vf"; depends=[assertthat BiocFileCache BiocSingular coda DirichletReg ggplot2 Matrix mclust purrr Rcpp RcppArmadillo RcppDist RcppProgress RCurl rhdf5 S4Vectors scales scater scran SingleCellExperiment SummarizedExperiment xgboost]; };
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BeadDataPackR = derive2 { name="BeadDataPackR"; version="1.48.0"; sha256="19f0y6drsrsrwysb16xx6mafgiw55fr35pwxkjxn0ks6jc5vx1cx"; depends=[]; };
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BgeeCall = derive2 { name="BgeeCall"; version="1.12.0"; sha256="0lwfcrzl048bn6jilx0ls29y6nnss66f7nr673h7m5962ay61mwp"; depends=[biomaRt Biostrings data_table dplyr GenomicFeatures jsonlite rhdf5 rslurm rtracklayer sjmisc tximport]; };
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BgeeDB = derive2 { name="BgeeDB"; version="2.22.0"; sha256="093zk43x8i9ajaqsdhndkyal3dizllr3g85ziavb3k73dzvarzsc"; depends=[Biobase curl data_table digest dplyr graph R_utils RCurl RSQLite tidyr topGO]; };
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BgeeCall = derive2 { name="BgeeCall"; version="1.12.1"; sha256="1g12cms66zb45p347h3b358vjhnq76galvwqwq86xby4hnwpdzkh"; depends=[biomaRt Biostrings data_table dplyr GenomicFeatures jsonlite rhdf5 rslurm rtracklayer sjmisc tximport]; };
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BgeeDB = derive2 { name="BgeeDB"; version="2.22.2"; sha256="0i7g1vmkn31r6abjsbhaiq4pz3p9zvpmlg2ykd1g7c2mqc7x8gc9"; depends=[Biobase curl data_table digest dplyr graph R_utils RCurl RSQLite tidyr topGO]; };
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BiFET = derive2 { name="BiFET"; version="1.16.0"; sha256="03ypbbn8i0f4bl4m6wfdcv702jydniak56wqjb1vlrckd9aphwzq"; depends=[GenomicRanges poibin]; };
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BiGGR = derive2 { name="BiGGR"; version="1.32.0"; sha256="0n57bgl6xz5b1gpw4isimq2pqxmlabn7jzhbjg2fbxcklabdvrcw"; depends=[hyperdraw hypergraph LIM limSolve rsbml stringr]; };
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BiRewire = derive2 { name="BiRewire"; version="3.28.0"; sha256="0r3i7n45qgj8wzdsx8wmfk0lc4xbcvxvmfziiqzig7r706q2c2hm"; depends=[igraph Matrix Rtsne slam]; };
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@ -103,7 +103,7 @@ in with self; {
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BioNERO = derive2 { name="BioNERO"; version="1.4.0"; sha256="1nyzjbl0gcwvbj2nxfwykirikf8j3rsx5ny45bqjbcb4r23k65kj"; depends=[BiocParallel ComplexHeatmap DESeq2 dynamicTreeCut GENIE3 ggnetwork ggnewscale ggplot2 ggpubr igraph intergraph matrixStats minet NetRep networkD3 RColorBrewer reshape2 SummarizedExperiment sva WGCNA]; };
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BioNet = derive2 { name="BioNet"; version="1.56.0"; sha256="0kcw71j4nmdkn373wk21ak6h0v4gycivnfrklb72kk1qcmsy1wrm"; depends=[AnnotationDbi Biobase graph igraph RBGL]; };
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BioNetStat = derive2 { name="BioNetStat"; version="1.16.0"; sha256="0f387j35lj32ryiw48jz8gc08al2lmmv9zvbbgyjq9wmqlca3dfb"; depends=[BiocParallel DT ggplot2 Hmisc igraph knitr markdown pathview pheatmap plyr psych RColorBrewer RJSONIO rmarkdown shiny shinyBS whisker yaml]; };
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BioPlex = derive2 { name="BioPlex"; version="1.2.0"; sha256="08688yjmvqgdzhxxlx0nxcfzsbfg92z0bnbq37aicldzmk9l9h00"; depends=[BiocFileCache GenomeInfoDb GenomicRanges GEOquery graph SummarizedExperiment]; };
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BioPlex = derive2 { name="BioPlex"; version="1.2.3"; sha256="0cn0x6ij2a3xy61bq0qy5amp0ipj4r4shh7g0vlwbkrclj9w347r"; depends=[BiocFileCache GenomeInfoDb GenomicRanges GEOquery graph SummarizedExperiment]; };
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BioQC = derive2 { name="BioQC"; version="1.24.0"; sha256="0vb2nnzqvyv25pw8qshcmijravswafg0858pkgqjgiv7wsr2mn3m"; depends=[Biobase edgeR Rcpp]; };
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BioTIP = derive2 { name="BioTIP"; version="1.10.0"; sha256="1sihi5zy7mlabh3ix1wvdqz8ibfq1avl8bnxjhvxyzq40zbcklh6"; depends=[cluster GenomicRanges igraph MASS psych scran stringr]; };
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Biobase = derive2 { name="Biobase"; version="2.56.0"; sha256="1mnxky78an079p60427cjvk4fzilp0xzy6b85fq274qvdcrz8jbv"; depends=[BiocGenerics]; };
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@ -114,11 +114,11 @@ in with self; {
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BiocIO = derive2 { name="BiocIO"; version="1.6.0"; sha256="16j826w4zrmbgpmq6nyglcrjailsfv48ih1rz1qn383g7v503ydp"; depends=[BiocGenerics S4Vectors]; };
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BiocNeighbors = derive2 { name="BiocNeighbors"; version="1.14.0"; sha256="1a43hzmcpxviqa9723hkafr6gm358amfpqj9d56imclkkfkdz95x"; depends=[BiocParallel Matrix Rcpp RcppHNSW S4Vectors]; };
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BiocOncoTK = derive2 { name="BiocOncoTK"; version="1.16.0"; sha256="1alplszw84vqa1mvzp996f94s40scmh4qwbrqhg43hrnyvbnq7pi"; depends=[bigrquery car ComplexHeatmap curatedTCGAData DBI dplyr DT GenomicFeatures GenomicRanges ggplot2 ggpubr graph httr IRanges magrittr plyr Rgraphviz rjson S4Vectors scales shiny SummarizedExperiment]; };
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BiocParallel = derive2 { name="BiocParallel"; version="1.30.0"; sha256="0krirrlxprcx3m4zl1lqr6mrm3w07xy3216iszvv47nfqq845mbb"; depends=[BH futile_logger snow]; };
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BiocParallel = derive2 { name="BiocParallel"; version="1.30.3"; sha256="1rs3wmasl9mx7f399iclvm0bnvggvjj2a88zbi294r5m8wxqlc92"; depends=[BH codetools futile_logger snow]; };
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BiocPkgTools = derive2 { name="BiocPkgTools"; version="1.14.0"; sha256="1v0824vmg49q9lh0igdyniryyknw6vmh462rn25kmg9hdna0w99h"; depends=[BiocFileCache BiocManager biocViews dplyr DT gh graph htmltools htmlwidgets httr igraph jsonlite magrittr RBGL readr rlang rvest stringr tibble tidyr tidyselect xml2]; };
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BiocSet = derive2 { name="BiocSet"; version="1.10.0"; sha256="1ghba7020inrdxlbrrgds9gjymjxjma2p89b9lgkjin89zalqglh"; depends=[AnnotationDbi BiocIO dplyr KEGGREST ontologyIndex plyr rlang S4Vectors tibble tidyr]; };
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BiocSingular = derive2 { name="BiocSingular"; version="1.12.0"; sha256="1sraycnn0jahpi8kni1y8ik00ga89fvwqjmbr8388968q22mvm3x"; depends=[beachmat BiocGenerics BiocParallel DelayedArray irlba Matrix Rcpp rsvd S4Vectors ScaledMatrix]; };
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BiocSklearn = derive2 { name="BiocSklearn"; version="1.18.0"; sha256="18qx1rpym845pa0kzrx6cmcdjng17inc2qa131apymrgfndgqa7y"; depends=[basilisk knitr Rcpp reticulate SummarizedExperiment]; };
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BiocSklearn = derive2 { name="BiocSklearn"; version="1.18.2"; sha256="0q9qlp12ycmhnvfqwn7mvrhd8ypwnbbf715ficgx1xnagh72dpgg"; depends=[basilisk reticulate SummarizedExperiment]; };
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BiocStyle = derive2 { name="BiocStyle"; version="2.24.0"; sha256="1nwiib201b9q1x19ihqjqr5jl0vnid8wfgpi8sa3y02bn722g5a5"; depends=[BiocManager bookdown knitr rmarkdown yaml]; };
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BiocVersion = derive2 { name="BiocVersion"; version="3.15.2"; sha256="0rs4nyza4hqqk204d037gi013135wgfhx5asq2dsdjc9vk5nwzfn"; depends=[]; };
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BiocWorkflowTools = derive2 { name="BiocWorkflowTools"; version="1.22.0"; sha256="1jj4icpkhrv9f6yx3vghkpdil1pfghf3yvc9756wmndvhs100r5l"; depends=[BiocStyle bookdown git2r httr knitr rmarkdown rstudioapi stringr usethis]; };
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@ -138,7 +138,7 @@ in with self; {
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CAGEr = derive2 { name="CAGEr"; version="2.2.0"; sha256="03gxnbsf8byk1ggijf264p6dyvl09hihkmrcx5m28pjs0imlzmhw"; depends=[BiocGenerics BiocParallel BSgenome data_table DelayedArray DelayedMatrixStats formula_tools GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 gtools IRanges KernSmooth memoise MultiAssayExperiment plyr reshape2 Rsamtools rtracklayer S4Vectors som stringdist stringi SummarizedExperiment vegan VGAM]; };
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CAMERA = derive2 { name="CAMERA"; version="1.52.0"; sha256="0jz8i0m8g8f18yzjzkgf4xsk038nm6h6qdhsdmmkprz97ysjayr5"; depends=[Biobase graph Hmisc igraph RBGL xcms]; };
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CARNIVAL = derive2 { name="CARNIVAL"; version="2.6.0"; sha256="0b0w2ijpv9mv2hiy82wl6lnpwxh30384c675748naq77ss93k8qr"; depends=[dplyr igraph lpSolve readr rjson rmarkdown stringr tibble tidyr]; };
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CATALYST = derive2 { name="CATALYST"; version="1.20.0"; sha256="156c5rdc1s84m6fwhwifwk603qwscw29dyvrni9ah9q2iz0xb4hm"; depends=[circlize ComplexHeatmap ConsensusClusterPlus cowplot data_table dplyr drc flowCore FlowSOM ggplot2 ggrepel ggridges gridExtra magrittr Matrix matrixStats nnls purrr RColorBrewer reshape2 Rtsne S4Vectors scales scater SingleCellExperiment SummarizedExperiment]; };
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CATALYST = derive2 { name="CATALYST"; version="1.20.1"; sha256="05vfqwa9qsm16px77s9bzygs6zymcxshymmpvz86a9l1cy1yxbza"; depends=[circlize ComplexHeatmap ConsensusClusterPlus cowplot data_table dplyr drc flowCore FlowSOM ggplot2 ggrepel ggridges gridExtra magrittr Matrix matrixStats nnls purrr RColorBrewer reshape2 Rtsne S4Vectors scales scater SingleCellExperiment SummarizedExperiment]; };
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CAnD = derive2 { name="CAnD"; version="1.27.0"; sha256="14x0m5iv7dm1iii5zsny9wnf4j5ddh0kij2jm658r3i4wnc99mkb"; depends=[ggplot2 reshape]; };
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CBEA = derive2 { name="CBEA"; version="1.0.0"; sha256="08hhpd7syycliqn5fw3x6pfxi89pghm4b4my4p73lvgkr75n71x4"; depends=[BiocParallel BiocSet dplyr fitdistrplus generics glue goftest lmom magrittr mixtools Rcpp rlang SummarizedExperiment tibble tidyr TreeSummarizedExperiment]; };
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CCPROMISE = derive2 { name="CCPROMISE"; version="1.22.0"; sha256="1zmm22rbwp706l2xl5623aja0fw01r0w9cn3dv8ga0riz3pz2fy7"; depends=[Biobase CCP GSEABase PROMISE]; };
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@ -149,14 +149,14 @@ in with self; {
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CGHcall = derive2 { name="CGHcall"; version="2.58.0"; sha256="1qpsibp4gb09sn6fkwwrdjkh3a28lqfbk18c6fvn4m386j96ps65"; depends=[Biobase CGHbase DNAcopy impute snowfall]; };
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CGHnormaliter = derive2 { name="CGHnormaliter"; version="1.50.0"; sha256="16i0i83wd3ibzkj5l5az3jxgsp78i6ragl3yiy3yymvgr9f2z3fz"; depends=[Biobase CGHbase CGHcall]; };
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CGHregions = derive2 { name="CGHregions"; version="1.54.0"; sha256="18k833qpbkyj8ywvgmglcxm3cqaj1ys4ygq7cvnv43d6sm4fi44m"; depends=[Biobase CGHbase]; };
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CHRONOS = derive2 { name="CHRONOS"; version="1.24.0"; sha256="0n1qm5d2xh00v49h91pzqmjyklp1wnf524fbglahh9kxbpq5fh8m"; depends=[biomaRt circlize doParallel foreach graph igraph openxlsx RBGL RCurl rJava XML]; };
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CHRONOS = derive2 { name="CHRONOS"; version="1.24.1"; sha256="1xkjliliwq03qklhcsvm2sbw6hprvzwid2cccb5zyx6gap7kszaz"; depends=[biomaRt circlize doParallel foreach graph igraph openxlsx RBGL RCurl rJava XML]; };
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CIMICE = derive2 { name="CIMICE"; version="1.4.0"; sha256="12knj9vz41kbx0jzqw6ah1ils6hsxv5fbnw98mbi3phnr3kl9ih4"; depends=[assertthat dplyr expm ggcorrplot ggplot2 ggraph glue igraph maftools Matrix networkD3 purrr tidygraph tidyr visNetwork]; };
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CINdex = derive2 { name="CINdex"; version="1.24.0"; sha256="1k6wl4y4za85n8pf96x9zj7irmq3glkpyz612wxj1s16whl6wy6s"; depends=[bitops dplyr GenomeInfoDb GenomicRanges gplots gridExtra IRanges png S4Vectors som stringr]; };
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CMA = derive2 { name="CMA"; version="1.54.0"; sha256="0bl8j1dx153k66vvmhsln1s58jnjfrp6ihfnydsgiq72zqkxhcbz"; depends=[Biobase]; };
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CNAnorm = derive2 { name="CNAnorm"; version="1.42.0"; sha256="1cnf8lj16d1z663ff4k5vfq4bkyj1jims6a6phkjj1sb1zsx3xji"; depends=[DNAcopy]; };
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CNEr = derive2 { name="CNEr"; version="1.32.0"; sha256="05zvr5fv8nprxqh2wvvrlf737dq242i20p1rpyqjaxihl6xl62kq"; depends=[annotate BiocGenerics Biostrings DBI GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 GO_db IRanges KEGGREST poweRlaw R_utils readr reshape2 RSQLite rtracklayer S4Vectors XVector]; };
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CNORdt = derive2 { name="CNORdt"; version="1.38.0"; sha256="161qhpx6kyn87h1p72mwfpi1pd4ck3cssr4f291axhw99sg6968c"; depends=[abind CellNOptR]; };
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CNORfeeder = derive2 { name="CNORfeeder"; version="1.35.0"; sha256="0z6j6rrlxpijd9vb2n6bgcy82w1w82rrzrhzrx7q9dgphblc7ag9"; depends=[CellNOptR graph]; };
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CNORfeeder = derive2 { name="CNORfeeder"; version="1.36.1"; sha256="07k18izfzfnm7l5bddbdyhignv18fgv3varvi8ynv22zd0gf9bs1"; depends=[CellNOptR graph]; };
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CNORfuzzy = derive2 { name="CNORfuzzy"; version="1.38.0"; sha256="0qnfvfd2wsmpaggq2amp8n1ry7wgysxysfh97rvrx5ymivbzr18p"; depends=[CellNOptR nloptr]; };
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CNORode = derive2 { name="CNORode"; version="1.38.0"; sha256="0bvlwlf0mm6q3cp2vf87rb7xsha5cz9bk7vsi6ssxngmspiq3kjz"; depends=[CellNOptR genalg knitr]; };
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CNTools = derive2 { name="CNTools"; version="1.52.0"; sha256="1d5ahszdf0brbmhd1vi2l9v1qi8kbpkw2kawcdf3rxibla0756y3"; depends=[genefilter]; };
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@ -183,7 +183,7 @@ in with self; {
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CSSQ = derive2 { name="CSSQ"; version="1.8.0"; sha256="1kgadkqjcac127xbaxr38r2icfhdz6y4q1w9xpamj4mjb6d27hq7"; depends=[GenomicAlignments GenomicFeatures GenomicRanges ggplot2 IRanges Rsamtools rtracklayer S4Vectors SummarizedExperiment]; };
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CTDquerier = derive2 { name="CTDquerier"; version="2.3.1"; sha256="18pxg4qhgf03sq48yp5m0x0jq5y27pbpqqlcvpn2pj09dzx7camc"; depends=[BiocFileCache ggplot2 gridExtra igraph RCurl S4Vectors stringdist stringr]; };
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CancerInSilico = derive2 { name="CancerInSilico"; version="2.16.0"; sha256="1xswflpx055x3lkakbvxaw6q8y4ndrpr9ma1wyia63ghvdnaian0"; depends=[BH Rcpp]; };
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CancerSubtypes = derive2 { name="CancerSubtypes"; version="1.22.0"; sha256="1qgjzbppi5nzw7jvqd0i780fccwz0mf5i6r4shzdnkvszh8q98a7"; depends=[cluster ConsensusClusterPlus iCluster impute limma NMF sigclust survival]; };
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CancerSubtypes = derive2 { name="CancerSubtypes"; version="1.22.0"; sha256="1qgjzbppi5nzw7jvqd0i780fccwz0mf5i6r4shzdnkvszh8q98a7"; depends=[cluster ConsensusClusterPlus impute limma NMF sigclust survival]; };
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Cardinal = derive2 { name="Cardinal"; version="2.14.0"; sha256="07048rzp4x6593836a9iag8xjq93a94z9zvj6cbp0bj15w3p62r6"; depends=[Biobase BiocGenerics BiocParallel dplyr EBImage irlba lattice magrittr Matrix matter mclust nlme ProtGenerics S4Vectors signal sp viridisLite]; };
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Category = derive2 { name="Category"; version="2.62.0"; sha256="07js03cfdd6gzbzw14iavlqxynfcqszh988v6k1a3h074wxiivqd"; depends=[annotate AnnotationDbi Biobase BiocGenerics DBI genefilter graph GSEABase Matrix RBGL]; };
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CausalR = derive2 { name="CausalR"; version="1.28.0"; sha256="1ij6z12a6irbd1hd8nzd01xipmrgrpj7gqm6gp5r3hd7gfdpsway"; depends=[igraph]; };
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@ -192,7 +192,7 @@ in with self; {
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CellBench = derive2 { name="CellBench"; version="1.12.0"; sha256="1sw3z3n7vdvw2352amc7biz35dmyzx7fhxdmz1jr0gdf0fhwhr1s"; depends=[BiocFileCache BiocGenerics BiocParallel dplyr glue lubridate magrittr memoise purrr rappdirs rlang SingleCellExperiment tibble tidyr tidyselect]; };
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CellMapper = derive2 { name="CellMapper"; version="1.22.0"; sha256="1sz81czvam86am9mrzs3kn4qn0qz6402i7n2bdic7hcchl00qbbd"; depends=[S4Vectors]; };
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CellMixS = derive2 { name="CellMixS"; version="1.12.0"; sha256="06xjxdgmgndc06xvgg1kylnh8248j780r4jbc27hga6jha9jbh1f"; depends=[BiocGenerics BiocNeighbors BiocParallel cowplot dplyr ggplot2 ggridges kSamples magrittr purrr scater SingleCellExperiment SummarizedExperiment tidyr viridis]; };
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CellNOptR = derive2 { name="CellNOptR"; version="1.42.0"; sha256="03p0z6ydw2fphayzzks31kmbsfhys4jis1527c0xw00byf9k6319"; depends=[ggplot2 graph igraph RBGL RCurl Rgraphviz stringi stringr XML]; };
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CellNOptR = derive2 { name="CellNOptR"; version="1.42.1"; sha256="0hacmjg02hz9qjk0dj95pwg3670gkvy22hs1wlvkrkicmwk4746r"; depends=[ggplot2 graph igraph RBGL RCurl Rgraphviz rmarkdown stringi stringr XML]; };
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CellScore = derive2 { name="CellScore"; version="1.16.0"; sha256="11iqs9isggfp5l1sh9ndsrb5f57lhgpspsb5mmzd1vn182bsj3n8"; depends=[Biobase gplots lsa RColorBrewer squash]; };
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CellTrails = derive2 { name="CellTrails"; version="1.14.0"; sha256="11xrkib9ajwsyz608d221r2z0nb67063ssmwd6i2zd4i7vhci5b0"; depends=[Biobase BiocGenerics cba dendextend dtw EnvStats ggplot2 ggrepel igraph maptree mgcv reshape2 Rtsne SingleCellExperiment SummarizedExperiment]; };
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CellaRepertorium = derive2 { name="CellaRepertorium"; version="1.6.0"; sha256="0ccx0698rircn5csd56il1v4s0707fhp2b7yidadrn6apv0jyd7b"; depends=[BiocGenerics Biostrings dplyr forcats Matrix progress purrr Rcpp reshape2 rlang S4Vectors stringr tibble tidyr]; };
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@ -206,7 +206,7 @@ in with self; {
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ChIPXpress = derive2 { name="ChIPXpress"; version="1.40.0"; sha256="1w8kvpvvwh7bjpk4672060vz0nn6ya0lm40k97grss1i4kmv7zna"; depends=[affy biganalytics bigmemory Biobase ChIPXpressData frma GEOquery]; };
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ChIPanalyser = derive2 { name="ChIPanalyser"; version="1.18.0"; sha256="0vi7qngbyss7h6zzbqv5x31x09pnwkrhxgfsbmhazz6wczmwkcix"; depends=[BiocManager Biostrings BSgenome GenomeInfoDb GenomicRanges IRanges RcppRoll ROCR rtracklayer S4Vectors]; };
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ChIPexoQual = derive2 { name="ChIPexoQual"; version="1.20.0"; sha256="1r4s8awvwwj1g33jpnzfxji23mfy0chkhi14i0ml5sh090xijpaz"; depends=[BiocParallel biovizBase broom data_table dplyr GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 hexbin IRanges RColorBrewer rmarkdown Rsamtools S4Vectors scales viridis]; };
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ChIPpeakAnno = derive2 { name="ChIPpeakAnno"; version="3.30.0"; sha256="1ch636j3zd6hcfnl455vjs36wffrdhwzyvkbikcwjg7idiknjdkf"; depends=[AnnotationDbi BiocGenerics biomaRt Biostrings DBI dplyr ensembldb GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 graph InteractionSet IRanges KEGGREST matrixStats multtest RBGL regioneR Rsamtools rtracklayer S4Vectors SummarizedExperiment VennDiagram]; };
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ChIPpeakAnno = derive2 { name="ChIPpeakAnno"; version="3.30.1"; sha256="0a26glldxczcfymjvd45gv5m4hympziivm6wwx4ab9wld7n43l8y"; depends=[AnnotationDbi BiocGenerics biomaRt Biostrings DBI dplyr ensembldb GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 graph InteractionSet IRanges KEGGREST matrixStats multtest RBGL regioneR Rsamtools rtracklayer S4Vectors SummarizedExperiment VennDiagram]; };
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ChIPseeker = derive2 { name="ChIPseeker"; version="1.32.0"; sha256="001f85nk4myk9vgs05inlj2dfby4802p1iyzkfqg332yk52gsbl7"; depends=[AnnotationDbi BiocGenerics boot dplyr enrichplot GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 gplots gtools IRanges magrittr plotrix RColorBrewer rtracklayer S4Vectors TxDb_Hsapiens_UCSC_hg19_knownGene]; };
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ChIPseqR = derive2 { name="ChIPseqR"; version="1.50.0"; sha256="09z03ym6iqllj007558pijksjz6bqizrq8r5y1s9f12919szydsv"; depends=[BiocGenerics Biostrings fBasics GenomicRanges HilbertVis IRanges S4Vectors ShortRead timsac]; };
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ChIPsim = derive2 { name="ChIPsim"; version="1.50.0"; sha256="1rjh61721pxm3r0zh1jpk65f2ll7yyhk7d92hvp4hjmq8283xwsh"; depends=[Biostrings IRanges ShortRead XVector]; };
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@ -216,7 +216,7 @@ in with self; {
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ChromHeatMap = derive2 { name="ChromHeatMap"; version="1.50.0"; sha256="1k7w5dlq5wa87rnqizvpr1pj3dx4l1ja6fls0691793ag337av0l"; depends=[annotate AnnotationDbi Biobase BiocGenerics GenomicRanges IRanges rtracklayer]; };
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ChromSCape = derive2 { name="ChromSCape"; version="1.6.0"; sha256="0hvk0lpslmlbim3dlr8rngp6ggr8chn2wbx344mf71hy48qyvarh"; depends=[batchelor BiocParallel colorRamps colourpicker ConsensusClusterPlus coop DelayedArray dplyr DT edgeR forcats fs GenomicRanges gggenes ggplot2 ggrepel gridExtra IRanges irlba jsonlite kableExtra Matrix matrixTests msigdbr plotly qs qualV Rcpp rlist Rsamtools rtracklayer Rtsne S4Vectors scater scran shiny shinycssloaders shinydashboard shinydashboardPlus shinyFiles shinyhelper shinyjs shinyWidgets SingleCellExperiment stringdist SummarizedExperiment tibble tidyr umap viridis]; };
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CiteFuse = derive2 { name="CiteFuse"; version="1.8.0"; sha256="19l1splp6364wfmddxxpj2zlq30frglzcrfs3xhkrai2yfx2cnmy"; depends=[cowplot dbscan ggplot2 ggraph ggridges gridExtra igraph Matrix mixtools pheatmap propr randomForest reshape2 rhdf5 rlang Rtsne S4Vectors scales scran SingleCellExperiment SummarizedExperiment uwot]; };
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ClassifyR = derive2 { name="ClassifyR"; version="3.0.2"; sha256="1x9bdx5jrdx0d1n3mlf1n67z39y4nr4izzw80fi62rgbfyb1pl8k"; depends=[BiocParallel dplyr MultiAssayExperiment randomForest rlang S4Vectors survival tidyr]; };
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ClassifyR = derive2 { name="ClassifyR"; version="3.0.3"; sha256="1a24i413v2cvmcf9f20gdvdkvwjx2yvlhbiasiwnmflb0p95n48m"; depends=[BiocParallel dplyr MultiAssayExperiment randomForest rlang S4Vectors survival tidyr]; };
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Clomial = derive2 { name="Clomial"; version="1.32.0"; sha256="0l1z45yp02hqjrrbyggk78fcm8g25sgdqsy4z2s4b2phrjh8nlc2"; depends=[matrixStats permute]; };
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Clonality = derive2 { name="Clonality"; version="1.44.0"; sha256="08z691r97krlzxwzcfhqkcpjwiacdxlfds1g4nzzi680zmvrdb4n"; depends=[DNAcopy]; };
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CluMSID = derive2 { name="CluMSID"; version="1.12.0"; sha256="0g9ml6dw5flcjlqjr4y33dy17hz2g9r7kavhywzgzh4167ppi0vh"; depends=[ape Biobase dbscan GGally ggplot2 gplots MSnbase mzR network plotly RColorBrewer S4Vectors sna]; };
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@ -228,11 +228,11 @@ in with self; {
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Cogito = derive2 { name="Cogito"; version="1.2.0"; sha256="0sahx7cdqqnpzwb0164c84xwr246aiv4jdv9b07mw3k4s45z3h37"; depends=[AnnotationDbi BiocManager entropy GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 jsonlite magrittr rmarkdown S4Vectors TxDb_Mmusculus_UCSC_mm9_knownGene]; };
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ComPrAn = derive2 { name="ComPrAn"; version="1.4.0"; sha256="0wwx025sv07h4xf3nvvqijvyca5mwdb8vsb8kvp4g0rxngc6jm30"; depends=[data_table dplyr DT forcats ggplot2 magrittr purrr RColorBrewer rio rlang scales shiny shinydashboard shinyjs stringr tibble tidyr VennDiagram]; };
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ComplexHeatmap = derive2 { name="ComplexHeatmap"; version="2.12.0"; sha256="15b49vlkl89prcw70mlw066z0gxhs26x8dpfn6qr3gz7hihygs65"; depends=[circlize clue codetools colorspace digest doParallel foreach GetoptLong GlobalOptions IRanges matrixStats png RColorBrewer]; };
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CompoundDb = derive2 { name="CompoundDb"; version="1.0.0"; sha256="0wgr6srhqd4gc97gxzk1np0y1pxa0sc01jsj34favmrvkryhh15j"; depends=[AnnotationFilter Biobase BiocGenerics ChemmineR DBI dbplyr dplyr IRanges jsonlite MetaboCoreUtils MsCoreUtils ProtGenerics RSQLite S4Vectors Spectra tibble xml2]; };
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CompoundDb = derive2 { name="CompoundDb"; version="1.0.1"; sha256="1f5x08adrkf71bwfa1vddzbmi0dya4i1wyjh51gjfd54cdg7g53i"; depends=[AnnotationFilter Biobase BiocGenerics ChemmineR DBI dbplyr dplyr IRanges jsonlite MetaboCoreUtils MsCoreUtils ProtGenerics RSQLite S4Vectors Spectra tibble xml2]; };
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ConsensusClusterPlus = derive2 { name="ConsensusClusterPlus"; version="1.60.0"; sha256="1021cix4mr9qsafskw4kk1l3wdzx9pk2gcwjifz6f4zqxss9v07p"; depends=[ALL Biobase cluster]; };
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CopyNumberPlots = derive2 { name="CopyNumberPlots"; version="1.12.0"; sha256="01sxmgsjrwhg8j7gckmcjwjy0yfbhw2rnww8z4hk0ig5vcb8g778"; depends=[cn_mops GenomeInfoDb GenomicRanges IRanges karyoploteR regioneR rhdf5 Rsamtools SummarizedExperiment VariantAnnotation]; };
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CopywriteR = derive2 { name="CopywriteR"; version="2.28.0"; sha256="1k11kvam96hpg71hz2n9cfzizmb7d1bmq5zfvm34s7fn09is60xb"; depends=[BiocParallel chipseq CopyhelpeR data_table DNAcopy futile_logger GenomeInfoDb GenomicAlignments GenomicRanges gtools IRanges matrixStats Rsamtools S4Vectors]; };
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CoreGx = derive2 { name="CoreGx"; version="2.0.0"; sha256="07p7za3qglwpsr6pvgjwcnwqzvd7v1rdnl55bqg0h5q893agz91i"; depends=[Biobase BiocGenerics BiocParallel BumpyMatrix checkmate crayon data_table glue lsa MatrixGenerics MultiAssayExperiment piano rlang S4Vectors SummarizedExperiment]; };
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CoreGx = derive2 { name="CoreGx"; version="2.0.2"; sha256="06wd9z8bgccxxxyipv30sgc2cxqnr1fmlpr3c11bqzaxp2g42y0a"; depends=[bench Biobase BiocGenerics BiocParallel BumpyMatrix checkmate crayon data_table glue lsa MatrixGenerics MultiAssayExperiment piano rlang S4Vectors SummarizedExperiment]; };
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Cormotif = derive2 { name="Cormotif"; version="1.42.0"; sha256="0ww39z987ig23sn9w2m7jd6rv3njiyslnzcxxzi6gbqy0dax8n93"; depends=[affy limma]; };
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CoverageView = derive2 { name="CoverageView"; version="1.34.0"; sha256="0mh66l4yh6rpd1r7qbqwh5jkklqyvpfiap0zcqhz9kimssm2pbbp"; depends=[GenomicAlignments GenomicRanges IRanges Rsamtools rtracklayer S4Vectors]; };
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CrispRVariants = derive2 { name="CrispRVariants"; version="1.24.0"; sha256="05hb0z6zmi6vxn11l5cih7ja92362v6idzwiwjk67dk4rrk273va"; depends=[AnnotationDbi BiocParallel Biostrings GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 gridExtra IRanges reshape2 Rsamtools S4Vectors]; };
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@ -242,7 +242,7 @@ in with self; {
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CytoML = derive2 { name="CytoML"; version="2.8.0"; sha256="0vp7advfh1d8596hjpzayasjhga4mx0l104sgz2asscbrjm4v7rr"; depends=[base64enc BH Biobase corpcor cytolib data_table dplyr flowCore flowWorkspace ggcyto graph jsonlite lattice openCyto plyr RBGL Rcpp RcppArmadillo RcppParallel Rgraphviz Rhdf5lib RProtoBufLib RUnit tibble XML xml2 yaml]; };
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CytoTree = derive2 { name="CytoTree"; version="1.6.0"; sha256="1dsdhwjkd3ngnw50fs6vz048afk47r95vhi0wqj8sip11nhndkd8"; depends=[Biobase BiocNeighbors cluster destiny flowCore FlowSOM flowUtils ggplot2 gmodels igraph limma Matrix matrixStats mclust pheatmap prettydoc RANN Rcpp Rtsne scatterpie scatterplot3d stringr sva umap]; };
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DAMEfinder = derive2 { name="DAMEfinder"; version="1.8.0"; sha256="123ra94bij0m45j2fzqr7fjipj4ld9kgk0kir1zfdbbd5h8h4mdf"; depends=[BiocGenerics Biostrings bumphunter cowplot GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 IRanges limma plyr readr reshape2 Rsamtools S4Vectors stringr SummarizedExperiment VariantAnnotation]; };
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DAPAR = derive2 { name="DAPAR"; version="1.28.0"; sha256="1349wcfn6bnsbjilkb3flidi1xklqi96rx6yf8f0gy8d4fxb433c"; depends=[Biobase Cairo cp4p DAPARdata dplyr ggplot2 gplots graph highcharter igraph imp4p impute knitr lattice limma lme4 Matrix MSnbase norm pcaMethods png preprocessCore RColorBrewer reshape2 scales siggenes stringr tibble tidyr tidyverse tmvtnorm]; };
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DAPAR = derive2 { name="DAPAR"; version="1.28.1"; sha256="1qhh9zipiwrm511wqb42d3bm2lz3h8bvyd6g6wyrgkj3730jg35f"; depends=[Biobase Cairo cp4p DAPARdata dplyr ggplot2 gplots graph highcharter igraph imp4p impute knitr lattice limma lme4 Matrix MSnbase norm pcaMethods png preprocessCore RColorBrewer reshape2 scales siggenes stringr tibble tidyr tidyverse tmvtnorm]; };
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DART = derive2 { name="DART"; version="1.44.0"; sha256="105f3awf9dxkmrqgxjqzsragvhavfnygzgggi0mgq330ybmmp1as"; depends=[igraph]; };
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DECIPHER = derive2 { name="DECIPHER"; version="2.24.0"; sha256="045q2bfzgq1yzhyrzvrhrnmlpka4gikrajxxwv05szksy5nvp7q5"; depends=[Biostrings DBI IRanges RSQLite S4Vectors XVector]; };
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DEComplexDisease = derive2 { name="DEComplexDisease"; version="1.16.0"; sha256="09a967x1rnv7byjwh29ngjhs67rgg27zblmlzx6pyqlwy5jsp89d"; depends=[BiocParallel ComplexHeatmap DESeq2 edgeR Rcpp SummarizedExperiment]; };
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@ -258,7 +258,7 @@ in with self; {
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DEqMS = derive2 { name="DEqMS"; version="1.14.0"; sha256="04b35mhsz87dfj53clgxrb7igkyv41hqmblb4429l68l55wsxhp6"; depends=[ggplot2 limma matrixStats]; };
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DEsingle = derive2 { name="DEsingle"; version="1.16.0"; sha256="0gw2zbq910jnn1pdpc5sgvvfmvg06hximz1qnvvmv9pb8g68r0zk"; depends=[bbmle BiocParallel gamlss MASS Matrix maxLik pscl VGAM]; };
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DEsubs = derive2 { name="DEsubs"; version="1.22.0"; sha256="06vjby0wpaczaw9bj2g2inylfnw92acrqgpadr70q458v1kpshs5"; depends=[circlize DESeq2 EBSeq edgeR ggplot2 graph igraph jsonlite limma locfit Matrix NBPSeq pheatmap RBGL]; };
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DExMA = derive2 { name="DExMA"; version="1.4.0"; sha256="00njmrb78qpadf5rwcfiigvzchvha7ql9qdm4w1p0c1vbfp13f2l"; depends=[Biobase bnstruct DExMAdata GEOquery impute limma pheatmap plyr scales snpStats sva swamp]; };
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DExMA = derive2 { name="DExMA"; version="1.4.2"; sha256="1brjyg7s0bhh2vdaqrpbhvy0h2vn2v6yvmj9l0nbjrz2p9wm705b"; depends=[Biobase bnstruct DExMAdata GEOquery impute limma pheatmap plyr RColorBrewer scales snpStats sva swamp]; };
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DFP = derive2 { name="DFP"; version="1.54.0"; sha256="19xjvfymjclnd0ck7n7al3f54s7f8z3aszi35i0cavr7xj3cgrj5"; depends=[Biobase]; };
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DIAlignR = derive2 { name="DIAlignR"; version="2.4.0"; sha256="0mh27n8vsnsv10mq8jcslspyq86sfvwwgn8iib5w3f7qb47w5d7r"; depends=[ape bit64 data_table DBI dplyr ggplot2 magrittr mzR phangorn pracma Rcpp RcppEigen reticulate rlang RMSNumpress RSQLite signal tidyr zoo]; };
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DMCFB = derive2 { name="DMCFB"; version="1.10.0"; sha256="0wka5s820k0vfw87dfycnkbr3c41wm4rmylwnkm8c0azjda8n126"; depends=[arm benchmarkme BiocParallel data_table fastDummies GenomicRanges IRanges MASS matrixStats rtracklayer S4Vectors speedglm SummarizedExperiment tibble]; };
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@ -289,9 +289,9 @@ in with self; {
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DelayedTensor = derive2 { name="DelayedTensor"; version="1.2.0"; sha256="1paciar5cm61gx894awwxb7gzqnyiwmsfinfijff2qx210l0yz51"; depends=[BiocSingular DelayedArray DelayedRandomArray einsum HDF5Array irlba Matrix rTensor]; };
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DepInfeR = derive2 { name="DepInfeR"; version="1.0.0"; sha256="03qvgk20dgxa95gkv2ya2dibiwshda3ssl5f95x5nn06lfgzk6m0"; depends=[BiocParallel glmnet matrixStats]; };
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DepecheR = derive2 { name="DepecheR"; version="1.12.0"; sha256="0rixczdds5gpac50wap6s68kmpdj4208l38gcihkrysz5frbvqjp"; depends=[beanplot doSNOW dplyr FNN foreach ggplot2 gmodels gplots MASS matrixStats mixOmics moments Rcpp RcppEigen reshape2 robustbase viridis]; };
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DiffBind = derive2 { name="DiffBind"; version="3.6.0"; sha256="0c8hqmhyy0f88x9z2f29s275643b1x59i41cq91640lbs4rwvhrs"; depends=[amap apeglm ashr BiocParallel DESeq2 dplyr GenomicAlignments GenomicRanges ggplot2 ggrepel gplots GreyListChIP IRanges lattice limma locfit RColorBrewer Rcpp Rhtslib Rsamtools S4Vectors SummarizedExperiment systemPipeR]; };
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DiffBind = derive2 { name="DiffBind"; version="3.6.1"; sha256="0izlk8vmmal4dj0bjxhgzr25arfa9zgdv06rm70w7ylr0gl84pzr"; depends=[amap apeglm ashr BiocParallel DESeq2 dplyr GenomicAlignments GenomicRanges ggplot2 ggrepel gplots GreyListChIP IRanges lattice limma locfit RColorBrewer Rcpp Rhtslib Rsamtools S4Vectors SummarizedExperiment systemPipeR]; };
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DiffLogo = derive2 { name="DiffLogo"; version="2.20.0"; sha256="08dr3ah0gakdkv133ipw1ib2w1p84hild0s4y9kp8z51qg0zk7mn"; depends=[cba]; };
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DifferentialRegulation = derive2 { name="DifferentialRegulation"; version="1.0.0"; sha256="05x2wdmk4lifkm2051my04gprmicijnpmz561qqx6z9903phswdi"; depends=[BANDITS data_table doParallel doRNG foreach MASS Matrix Rcpp RcppArmadillo SingleCellExperiment SummarizedExperiment]; };
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DifferentialRegulation = derive2 { name="DifferentialRegulation"; version="1.0.5"; sha256="1wxf3zwx4yp58gn7yhzl2kp1ki5p80b6wrz2x5phh4k3s1qr1xnj"; depends=[BANDITS data_table doParallel doRNG foreach ggplot2 MASS Matrix Rcpp RcppArmadillo SingleCellExperiment SummarizedExperiment]; };
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Dino = derive2 { name="Dino"; version="1.2.0"; sha256="1rcll2y034v1n183v819brazr6crr73klp8qmkq51p7jpsvx1450"; depends=[BiocParallel BiocSingular Matrix matrixStats S4Vectors scran Seurat SingleCellExperiment SummarizedExperiment]; };
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Director = derive2 { name="Director"; version="1.22.0"; sha256="1s6yg90ai37cvkqq7gs394bxd70l85mgz36y6gyjv1bzbc298am8"; depends=[htmltools]; };
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DirichletMultinomial = derive2 { name="DirichletMultinomial"; version="1.38.0"; sha256="15l0h2qz80lmrm5rva3v7lkgddn42igyxxwims57zwpwyhrk9bmx"; depends=[BiocGenerics IRanges S4Vectors]; };
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@ -318,14 +318,14 @@ in with self; {
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ERSSA = derive2 { name="ERSSA"; version="1.14.0"; sha256="0g06svlww704z65jk9w747gs8jv6h75b9d096an0qi5zqp2s1lh4"; depends=[BiocParallel DESeq2 edgeR ggplot2 plyr RColorBrewer]; };
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EWCE = derive2 { name="EWCE"; version="1.4.0"; sha256="19mq43s0rfzgy793cf7l5a4vgss3s2l0nhnsfgdsrxv4gy6nfgnq"; depends=[BiocParallel data_table DelayedArray dplyr ewceData ggplot2 HGNChelper limma Matrix orthogene reshape2 RNOmni SingleCellExperiment stringr SummarizedExperiment]; };
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EmpiricalBrownsMethod = derive2 { name="EmpiricalBrownsMethod"; version="1.24.0"; sha256="04r9fcxaqajhzdbjhi9dhv8pppqlprc0g5h2spf0d798if51f2ck"; depends=[]; };
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EnMCB = derive2 { name="EnMCB"; version="1.8.0"; sha256="1xksk71w3bywbkqyx7ypnz0r5xz6vp0ln43k83dfyaw71r4fyxzm"; depends=[BiocFileCache boot e1071 ggplot2 glmnet igraph Matrix mboost rms survival survivalROC survivalsvm]; };
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EnMCB = derive2 { name="EnMCB"; version="1.8.2"; sha256="1kna7s4rz5mlaj7vwc0mrzaziadvai7zq8ajiy4jya8xw78llyw4"; depends=[BiocFileCache boot e1071 ggplot2 glmnet igraph Matrix mboost rms survival survivalROC survivalsvm]; };
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EnhancedVolcano = derive2 { name="EnhancedVolcano"; version="1.14.0"; sha256="1ghsmfyhb2wa6vm5zhpjxcbmlnwhccahjajgpccbn85lq2203lz2"; depends=[ggplot2 ggrepel]; };
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EnrichedHeatmap = derive2 { name="EnrichedHeatmap"; version="1.26.0"; sha256="1960amh4pwnim6didgjqp6f3456ddndcsz2ghvpc0pv8v832phnl"; depends=[circlize ComplexHeatmap GenomicRanges GetoptLong IRanges locfit matrixStats Rcpp]; };
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EnrichmentBrowser = derive2 { name="EnrichmentBrowser"; version="2.26.0"; sha256="1bqq2jhlqm1vykrlr65z7yrvai406wymhrz0kallyhvgqwjbzwl3"; depends=[AnnotationDbi BiocFileCache BiocManager edgeR GO_db graph graphite GSEABase hwriter KEGGgraph KEGGREST limma pathview Rgraphviz S4Vectors safe SPIA SummarizedExperiment]; };
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EpiCompare = derive2 { name="EpiCompare"; version="1.0.0"; sha256="0ca4xh0slzhdbji5ffqgjvd9vgaypmgl412vksc8n1jg6q7zx0xm"; depends=[AnnotationHub BRGenomics ChIPseeker clusterProfiler dplyr genomation GenomicRanges ggplot2 IRanges magrittr org_Hs_eg_db plotly plyranges reshape2 rmarkdown rtracklayer S4Vectors stringr tidyr UpSetR]; };
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EpiDISH = derive2 { name="EpiDISH"; version="2.12.0"; sha256="020jimk1qy6r62z6pibsi9nyjxpfw0ikn1h136pn13b42rrrmjk4"; depends=[e1071 locfdr MASS Matrix matrixStats quadprog stringr]; };
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EpiTxDb = derive2 { name="EpiTxDb"; version="1.8.0"; sha256="12xa3h1j7jp1h27dz7hqfsbx3h4p76r5fm1bvspf52w8823qwpds"; depends=[AnnotationDbi BiocFileCache BiocGenerics Biostrings curl DBI GenomeInfoDb GenomicFeatures GenomicRanges httr IRanges Modstrings RSQLite S4Vectors tRNAdbImport xml2]; };
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EventPointer = derive2 { name="EventPointer"; version="3.3.1"; sha256="1nykyh45fasdy9m67f2m6kb6f73ycz4al10gfwcqv5694zp3vvrl"; depends=[abind affxparser Biostrings BSgenome cobs doParallel foreach GenomeInfoDb GenomicFeatures GenomicRanges glmnet graph igraph IRanges iterators limma lpSolve MASS Matrix matrixStats nnls poibin prodlim qvalue RBGL rhdf5 S4Vectors SGSeq speedglm stringr SummarizedExperiment tximport]; };
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EventPointer = derive2 { name="EventPointer"; version="3.4.1"; sha256="0fykvpbi4jr9j5xkbia7gj7yq3xf2nfahasa44i4yswqr7d82bbl"; depends=[abind affxparser Biostrings BSgenome cobs doParallel fgsea foreach GenomeInfoDb GenomicFeatures GenomicRanges glmnet graph igraph IRanges iterators limma lpSolve MASS Matrix matrixStats nnls poibin prodlim qvalue RBGL rhdf5 S4Vectors SGSeq speedglm stringr SummarizedExperiment tximport]; };
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ExCluster = derive2 { name="ExCluster"; version="1.14.0"; sha256="1vxkhll9zmv4w13xhazhmpbfjsc47g4sz2hizci491hyh41yq4jx"; depends=[GenomicRanges IRanges matrixStats Rsubread rtracklayer]; };
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ExiMiR = derive2 { name="ExiMiR"; version="2.38.0"; sha256="06k8f62c9ssbmqgx2gyxhy5cx8mryx3d5mzrwjlq35jbnnvdqn8c"; depends=[affy affyio Biobase limma preprocessCore]; };
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ExperimentHub = derive2 { name="ExperimentHub"; version="2.4.0"; sha256="11hna8vrm1az1zk7pw2dv0wh84sd0hw2bi55w40hqvs36csb7lkl"; depends=[AnnotationHub BiocFileCache BiocGenerics BiocManager curl rappdirs S4Vectors]; };
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@ -338,14 +338,14 @@ in with self; {
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FELLA = derive2 { name="FELLA"; version="1.16.0"; sha256="0j7h8xaxa0wkpbfwq17qgsp3rn45fkjv4fc3ca01y1kvj219a3vw"; depends=[igraph KEGGREST Matrix plyr]; };
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FGNet = derive2 { name="FGNet"; version="3.30.0"; sha256="10v82y7gmxxq1drw1w51r175ada5igy1ixj2m6y6kk8xldiy1ngr"; depends=[hwriter igraph plotrix png R_utils RColorBrewer reshape2 XML]; };
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FISHalyseR = derive2 { name="FISHalyseR"; version="1.30.0"; sha256="12qrqh9xm3zd2wlkda4n3h4v057hq3bgqzz8z25wnhxil6qyqb43"; depends=[abind EBImage]; };
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FLAMES = derive2 { name="FLAMES"; version="1.2.0"; sha256="0k5bz895lc7z6w49drckzmr0n413lqafyfqdwjc9zyqf0yaqxfnx"; depends=[bambu basilisk BiocGenerics Biostrings circlize ComplexHeatmap cowplot dplyr GenomeInfoDb GenomicFeatures GenomicRanges ggbio ggplot2 gridExtra igraph magrittr Matrix RColorBrewer Rcpp reticulate Rhtslib Rsamtools rtracklayer S4Vectors scater scran scuttle SingleCellExperiment stringr SummarizedExperiment tidyr withr zlibbioc]; };
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FLAMES = derive2 { name="FLAMES"; version="1.2.1"; sha256="0xyjqhkpyp0xm6jj0wymq9zd5vw4dx6szg12i1ck3p5w0szqldmd"; depends=[bambu basilisk BiocGenerics Biostrings circlize ComplexHeatmap cowplot dplyr GenomeInfoDb GenomicFeatures GenomicRanges ggbio ggplot2 gridExtra igraph magrittr Matrix RColorBrewer Rcpp reticulate Rhtslib Rsamtools rtracklayer S4Vectors scater scran scuttle SingleCellExperiment stringr SummarizedExperiment tidyr withr zlibbioc]; };
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FRASER = derive2 { name="FRASER"; version="1.8.0"; sha256="0qbysjhii7kq43c10zzjnky5dbcqa564mjk1pxf5ga16143zixd9"; depends=[AnnotationDbi BBmisc Biobase BiocGenerics BiocParallel biomaRt BSgenome cowplot data_table DelayedArray DelayedMatrixStats extraDistr generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 ggrepel HDF5Array IRanges matrixStats OUTRIDER pcaMethods pheatmap plotly PRROC R_utils RColorBrewer Rcpp RcppArmadillo rhdf5 Rsamtools Rsubread S4Vectors SummarizedExperiment tibble VGAM]; };
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FRGEpistasis = derive2 { name="FRGEpistasis"; version="1.32.0"; sha256="14wskfc350zrna1ng8wkyb91y3h01jhk93ajw3if04nkghav193a"; depends=[fda MASS]; };
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FScanR = derive2 { name="FScanR"; version="1.6.0"; sha256="0117fgbmig6zaik5j7axcw33rx2pjwhgla751sr4zi990a9p6igb"; depends=[]; };
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FamAgg = derive2 { name="FamAgg"; version="1.24.0"; sha256="0pzqy8rx7hyz93v8gh4qf861axwidxwiv3w9i8j7g796mdmy66my"; depends=[BiocGenerics gap igraph kinship2 Matrix survey]; };
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FastqCleaner = derive2 { name="FastqCleaner"; version="1.13.0"; sha256="140g8l2z2yvspz4cs01wbxd1k5bk36fmvdgbqx06y0qxyfprglzv"; depends=[Biostrings DT htmltools IRanges Rcpp S4Vectors shiny shinyBS ShortRead]; };
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FilterFFPE = derive2 { name="FilterFFPE"; version="1.6.0"; sha256="0x76a382lw0j06h8hlq2vrawnydjngn9w0dhymyrx94jkmsl15wl"; depends=[doParallel foreach GenomicRanges IRanges Rsamtools S4Vectors]; };
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FindIT2 = derive2 { name="FindIT2"; version="1.2.0"; sha256="0xbs8v2xj14ak5jqc55rr4iyk37riq6g4wgrhg0hcrljjbai14v2"; depends=[BiocGenerics BiocParallel dplyr GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 ggrepel glmnet IRanges MultiAssayExperiment patchwork progress purrr qvalue rlang rtracklayer S4Vectors stringr SummarizedExperiment tibble tidyr withr]; };
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FindIT2 = derive2 { name="FindIT2"; version="1.2.3"; sha256="0fj6csbxx6dfcd8fhsiff04cagb2yyg79h8wklqqm0dr7agbfaj9"; depends=[BiocGenerics BiocParallel dplyr GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 ggrepel glmnet IRanges MultiAssayExperiment patchwork progress purrr qvalue rlang rtracklayer S4Vectors stringr SummarizedExperiment tibble tidyr withr]; };
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FitHiC = derive2 { name="FitHiC"; version="1.22.0"; sha256="0iv14yx3g7shzl8qrjknyxbmiylj51sbd1wzr1ff9lc5shgl55kq"; depends=[data_table fdrtool Rcpp]; };
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FlowSOM = derive2 { name="FlowSOM"; version="2.4.0"; sha256="0balsds5mm981cqamdjv3ndq1y9arharisd6f2lrpkzgvwawa645"; depends=[BiocGenerics colorRamps ConsensusClusterPlus CytoML dplyr flowCore flowWorkspace ggforce ggnewscale ggplot2 ggpointdensity ggpubr ggrepel igraph magrittr pheatmap RColorBrewer rlang Rtsne scattermore tidyr XML]; };
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FoldGO = derive2 { name="FoldGO"; version="1.14.0"; sha256="1dwdppgawgc22qryc98p3ibamcn90871hgix1ad0p3zyhpvza9z5"; depends=[ggplot2 tidyr topGO]; };
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@ -359,7 +359,7 @@ in with self; {
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GCSConnection = derive2 { name="GCSConnection"; version="1.7.0"; sha256="1psmw3825whyzvbzqpqksgcl09b6kfyb8k5vny6ljkjbac1jzvnf"; depends=[googleAuthR googleCloudStorageR httr jsonlite Rcpp]; };
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GCSFilesystem = derive2 { name="GCSFilesystem"; version="1.6.0"; sha256="0qk8xyg06f71y4r1q1zpcj89irh9i6cd9z6nqlx635x8if84sh6d"; depends=[]; };
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GCSscore = derive2 { name="GCSscore"; version="1.10.0"; sha256="0cdhv2awcyg95cjwq088r9rsbmdi3vqnlnh0c74h7k2gjldl9r24"; depends=[affxparser Biobase BiocManager data_table devtools dplR RSQLite stringr]; };
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GDCRNATools = derive2 { name="GDCRNATools"; version="1.15.0"; sha256="1ifh8cwpvqv38xhh3mx8ly6y8dmd72dkll1fqyflz4bkjvhi5f0x"; depends=[BiocParallel biomaRt clusterProfiler DESeq2 DOSE DT edgeR GenomicDataCommons ggplot2 gplots jsonlite limma org_Hs_eg_db pathview rjson shiny survival survminer XML]; };
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GDCRNATools = derive2 { name="GDCRNATools"; version="1.16.2"; sha256="1zr1c32x8fj24mn240yx5v3q2p63j018hq90q06bh85y6jzq7zaw"; depends=[BiocParallel biomaRt clusterProfiler DESeq2 DOSE DT edgeR GenomicDataCommons ggplot2 gplots jsonlite limma org_Hs_eg_db pathview rjson shiny survival survminer XML]; };
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GDSArray = derive2 { name="GDSArray"; version="1.16.0"; sha256="1j6a0xlrx4cjqsfcm1k1vapddi5v2q5h05b617i839l9cp0ggd1s"; depends=[BiocGenerics DelayedArray gdsfmt S4Vectors SeqArray SNPRelate]; };
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GEM = derive2 { name="GEM"; version="1.22.0"; sha256="0vxpncvnqhgggy0is4lvgf29lgh307jkgz4zjjspdq9ds6y40l1i"; depends=[ggplot2]; };
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GENESIS = derive2 { name="GENESIS"; version="2.26.0"; sha256="1qn3x6j9lvyx130sx9wg7bxvacwbwp87x75inpxx9llc00p7sl9c"; depends=[Biobase BiocGenerics BiocParallel data_table gdsfmt GenomicRanges GWASTools igraph IRanges Matrix reshape2 S4Vectors SeqArray SeqVarTools SNPRelate]; };
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@ -367,7 +367,7 @@ in with self; {
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GEOexplorer = derive2 { name="GEOexplorer"; version="1.2.0"; sha256="00lnrp07nv8hia77riy3p10iq5rsyjzlrq93l4ql6m2cxv2p4qdg"; depends=[Biobase DT factoextra GEOquery ggplot2 heatmaply htmltools impute limma maptools pheatmap plotly scales shiny shinyBS shinybusy shinyHeatmaply stringr umap]; };
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GEOfastq = derive2 { name="GEOfastq"; version="1.4.0"; sha256="05s35fbzi2w3c4y11h144mf70i0rhbx1jwdz70ldyfa0ld3hbh89"; depends=[doParallel foreach plyr RCurl rvest stringr xml2]; };
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GEOmetadb = derive2 { name="GEOmetadb"; version="1.58.0"; sha256="12x2aabm2m1rv4s91h6vyq5q36i4i15lgh3bya3bjm80bfmxkfm3"; depends=[GEOquery RSQLite]; };
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GEOquery = derive2 { name="GEOquery"; version="2.64.0"; sha256="0n21k7p2z65yw2rgf24l7van9zg4jy8sck0xmkb2l9m7q457a6iz"; depends=[Biobase curl data_table dplyr limma magrittr R_utils readr tidyr xml2]; };
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GEOquery = derive2 { name="GEOquery"; version="2.64.2"; sha256="1cvkvq2haz831qi8w0gd3ayvxfxsl0z5klhki4gkfi9xqdv1gi9x"; depends=[Biobase curl data_table dplyr limma magrittr R_utils readr tidyr xml2]; };
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GEOsubmission = derive2 { name="GEOsubmission"; version="1.48.0"; sha256="0ml72djmli9qvq2c75nqq00q31lqcb64v8532vw4fk57cclmf76d"; depends=[affy Biobase]; };
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GEWIST = derive2 { name="GEWIST"; version="1.40.0"; sha256="0df1jm69krsr8y315mx93hjnmf4qpvnhbm0iz4j4920ra7g8wdp7"; depends=[car]; };
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GGPA = derive2 { name="GGPA"; version="1.8.0"; sha256="08p3k5dfkc2la5j99wbwswd7zhc4i4aynkmr3x561h6p59n31hnk"; depends=[GGally matrixStats network Rcpp RcppArmadillo scales sna]; };
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@ -386,7 +386,7 @@ in with self; {
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GOsummaries = derive2 { name="GOsummaries"; version="2.32.0"; sha256="0wkal7hsfz9msf8j7975vkqqzv5x681c891zj1b4mfk6dvn5xffa"; depends=[ggplot2 gProfileR gtable limma plyr Rcpp reshape2]; };
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GPA = derive2 { name="GPA"; version="1.8.0"; sha256="0z4qh88x7gvm02186mnl6bkhg1f5swqci30gzj27lj1kx700jsf3"; depends=[DT ggplot2 ggrepel plyr Rcpp shiny shinyBS vegan]; };
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GRENITS = derive2 { name="GRENITS"; version="1.48.0"; sha256="09c6d8hcawc6ky0pjhvc5yvd7fj1a1bl8n4hcw72nyfgbf20hygi"; depends=[ggplot2 Rcpp RcppArmadillo reshape2]; };
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GRaNIE = derive2 { name="GRaNIE"; version="1.0.0"; sha256="12fvk6lf7njd5d0j73xlg7jamrdyyvbjw6yxd7iq35snw2hvvixb"; depends=[BiocFileCache BiocManager BiocParallel Biostrings checkmate circlize colorspace ComplexHeatmap csaw data_table DESeq2 dplyr forcats futile_logger GenomeInfoDb GenomicRanges ggplot2 gridExtra igraph IRanges limma magrittr Matrix matrixStats patchwork progress purrr RColorBrewer readr reshape2 rlang robust S4Vectors scales stringr SummarizedExperiment tibble tidyr tidyselect tidyverse topGO viridis]; };
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GRaNIE = derive2 { name="GRaNIE"; version="1.0.2"; sha256="1csqlgkqmpsnjxajxklj3fn2k46gsa7fb8kah7k7irmjh0lsiqid"; depends=[BiocFileCache BiocManager BiocParallel Biostrings checkmate circlize colorspace ComplexHeatmap csaw data_table DESeq2 dplyr forcats futile_logger GenomeInfoDb GenomicRanges ggplot2 gridExtra igraph IRanges limma magrittr Matrix matrixStats patchwork progress purrr RColorBrewer readr reshape2 rlang robust S4Vectors scales stringr SummarizedExperiment tibble tidyr tidyselect tidyverse topGO viridis]; };
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GRmetrics = derive2 { name="GRmetrics"; version="1.22.0"; sha256="1qz2bj8wnp14mw5zm2207xk3zj98s2gk16fvhdzpy21y07irrx3j"; depends=[drc ggplot2 plotly S4Vectors SummarizedExperiment]; };
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GRridge = derive2 { name="GRridge"; version="1.20.0"; sha256="16bra2nz4i4f40x2gfcky7ggz3alpvhwcbilv48r7nv4p6b31j8i"; depends=[glmnet graph Iso mvtnorm penalized survival]; };
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GSALightning = derive2 { name="GSALightning"; version="1.24.0"; sha256="0p2k8k05283h7ls1aj5457ycqq46mxjjx7pmjijmj0kfzcmnqyv2"; depends=[data_table Matrix]; };
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@ -398,7 +398,7 @@ in with self; {
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GSEAmining = derive2 { name="GSEAmining"; version="1.6.0"; sha256="19r923086qr400f4p2kfn4ii09q2k2pqg9k4r035b9afqgd0x91a"; depends=[dendextend dplyr ggplot2 ggwordcloud gridExtra rlang stringr tibble tidytext]; };
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GSRI = derive2 { name="GSRI"; version="2.44.0"; sha256="0z79l6m3z0ib9iy24hpiscmxasrx33y6swrdg0k1z48sdhy0gsf1"; depends=[Biobase fdrtool genefilter GSEABase les]; };
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GSReg = derive2 { name="GSReg"; version="1.30.0"; sha256="0g0j4bh9h8qvki84gcp2s6yn2hhc38219jzihmf9jpjl66k74gs0"; depends=[AnnotationDbi GenomicFeatures Homo_sapiens org_Hs_eg_db]; };
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GSVA = derive2 { name="GSVA"; version="1.44.0"; sha256="01mpcc28a1lki969i0s7pxpz0xwxaiy76ikcs52bbabsjadpbclg"; depends=[Biobase BiocParallel BiocSingular DelayedArray DelayedMatrixStats GSEABase HDF5Array IRanges Matrix S4Vectors SingleCellExperiment sparseMatrixStats SummarizedExperiment]; };
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GSVA = derive2 { name="GSVA"; version="1.44.2"; sha256="0q0216hq3zfqxsirfllvs1p7zlpm8j7gg9mvlgyqz8yjfz6p02sq"; depends=[Biobase BiocParallel BiocSingular DelayedArray DelayedMatrixStats GSEABase HDF5Array IRanges Matrix S4Vectors SingleCellExperiment sparseMatrixStats SummarizedExperiment]; };
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GSgalgoR = derive2 { name="GSgalgoR"; version="1.6.0"; sha256="1wi6ww5rycc2zxhnm83amzrh7ffripmiqklcmxisv6jqgr64adp3"; depends=[cluster doParallel foreach matchingR nsga2R proxy survival]; };
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GUIDEseq = derive2 { name="GUIDEseq"; version="1.26.0"; sha256="1ar20zr3mjfqs7fvd323mdrxylvsjazn6si4d8ilgbpq4xhdv58a"; depends=[BiocGenerics BiocParallel Biostrings BSgenome ChIPpeakAnno CRISPRseek data_table dplyr GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges hash IRanges limma matrixStats Rsamtools S4Vectors]; };
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GWAS_BAYES = derive2 { name="GWAS.BAYES"; version="1.6.0"; sha256="01bj6gh95p95imyvvzjylnw42rcrzw3x8z0q8x2cx42zqf45dqc1"; depends=[caret doParallel GA ggplot2 Matrix memoise Rcpp RcppEigen reshape2]; };
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@ -406,7 +406,7 @@ in with self; {
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GWENA = derive2 { name="GWENA"; version="1.6.0"; sha256="10cs5csg6dwqajsk461flq55siz6jfd90w5cyqdhyq4mcbv6zp1x"; depends=[cluster dplyr dynamicTreeCut ggplot2 gprofiler2 igraph magrittr matrixStats NetRep purrr RColorBrewer rlist stringr SummarizedExperiment tibble tidyr WGCNA]; };
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GateFinder = derive2 { name="GateFinder"; version="1.16.0"; sha256="1wrx3rp1r4fjq8c56dk40izawzpsrmkrrdvivi67arx5pdjhjz30"; depends=[diptest flowCore flowFP mvoutlier splancs]; };
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GenProSeq = derive2 { name="GenProSeq"; version="1.0.0"; sha256="0vmsjpdkfvq28bihmf47a2ihlfxzadjr5vm6clh25016rz0086pp"; depends=[CatEncoders DeepPINCS keras mclust reticulate tensorflow ttgsea word2vec]; };
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GenVisR = derive2 { name="GenVisR"; version="1.28.0"; sha256="1cr9f044vj4qfb050nsbnnr9bvz12p3fzvnag54na3j2yinvsq6c"; depends=[AnnotationDbi BiocGenerics biomaRt Biostrings BSgenome data_table DBI FField GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 gridExtra gtable gtools IRanges plyr reshape2 Rsamtools scales VariantAnnotation viridis]; };
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GenVisR = derive2 { name="GenVisR"; version="1.28.0"; sha256="1cr9f044vj4qfb050nsbnnr9bvz12p3fzvnag54na3j2yinvsq6c"; depends=[AnnotationDbi BiocGenerics biomaRt Biostrings BSgenome data_table DBI GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 gridExtra gtable gtools IRanges plyr reshape2 Rsamtools scales VariantAnnotation viridis]; };
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GeneAccord = derive2 { name="GeneAccord"; version="1.14.0"; sha256="0lpw3fxfwfhnymivvjh6na9ssqs7268543kpf5wximfcm7wy9mzm"; depends=[biomaRt caTools dplyr ggplot2 ggpubr gtools magrittr maxLik RColorBrewer reshape2 tibble]; };
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GeneBreak = derive2 { name="GeneBreak"; version="1.26.0"; sha256="0dw5r5zaxp0y2g626gsvwcqcaqf7lz8ajnca6n6k6krbng7nqpf2"; depends=[CGHbase CGHcall GenomicRanges QDNAseq]; };
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GeneExpressionSignature = derive2 { name="GeneExpressionSignature"; version="1.42.0"; sha256="0jyxvsqm8gswbv2aky18hz2lc75l2l12yidhkqhv0c0rr3kxqvsv"; depends=[Biobase]; };
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@ -418,19 +418,19 @@ in with self; {
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GeneRegionScan = derive2 { name="GeneRegionScan"; version="1.52.0"; sha256="0qgfjlahc93ijsz7m2i11xmkkkwnzddf4mi17l2cq6a14ykdlww5"; depends=[affxparser Biobase Biostrings RColorBrewer S4Vectors]; };
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GeneSelectMMD = derive2 { name="GeneSelectMMD"; version="2.40.0"; sha256="19q88wy0gmyyvc9ddq7dm6mqy5zh8kqpad1dz5ymvzq8663cldqa"; depends=[Biobase limma MASS]; };
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GeneStructureTools = derive2 { name="GeneStructureTools"; version="1.16.0"; sha256="1ciflsp0i96ljh4xz1b1bbf6za4hd2swnykmp0wvgayxxcwxdwjv"; depends=[Biostrings BSgenome_Mmusculus_UCSC_mm10 data_table GenomicRanges Gviz IRanges plyr rtracklayer S4Vectors stringdist stringr]; };
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GeneTonic = derive2 { name="GeneTonic"; version="2.0.0"; sha256="17bk87n8i50qprwsh2ig5xyvbvf8qrii19k2d8hwpw1fa593h9sm"; depends=[AnnotationDbi backbone bs4Dash circlize colorspace colourpicker ComplexHeatmap ComplexUpset dendextend DESeq2 dplyr DT dynamicTreeCut expm ggforce ggplot2 ggrepel GO_db igraph matrixStats plotly RColorBrewer rintrojs rlang rmarkdown S4Vectors scales shiny shinyAce shinycssloaders shinyWidgets SummarizedExperiment tidyr tippy viridis visNetwork]; };
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GeneTonic = derive2 { name="GeneTonic"; version="2.0.1"; sha256="1k1b76d7cmfav3lyfxcyqgawjmnnk8c8p5qqgg970lnhlbf2351m"; depends=[AnnotationDbi backbone bs4Dash circlize colorspace colourpicker ComplexHeatmap ComplexUpset dendextend DESeq2 dplyr DT dynamicTreeCut expm ggforce ggplot2 ggrepel GO_db igraph matrixStats plotly RColorBrewer rintrojs rlang rmarkdown S4Vectors scales shiny shinyAce shinycssloaders shinyWidgets SummarizedExperiment tidyr tippy viridis visNetwork]; };
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GeneticsPed = derive2 { name="GeneticsPed"; version="1.58.0"; sha256="0vbkbjyb9r5gsbkn3c28y3bicmn82r1bfsah6ww6pf539xzipbzj"; depends=[gdata genetics MASS]; };
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GenomeInfoDb = derive2 { name="GenomeInfoDb"; version="1.32.1"; sha256="0iq6rgyxq17kzpikzhhh04ydpd5g9b71qbm879b033xlxrp6kxym"; depends=[BiocGenerics GenomeInfoDbData IRanges RCurl S4Vectors]; };
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GenomeInfoDb = derive2 { name="GenomeInfoDb"; version="1.32.2"; sha256="1n37bwb2fqmdgqbn19rgsd2qn8vbdhv6khdwjr7v12bwabcbx9xh"; depends=[BiocGenerics GenomeInfoDbData IRanges RCurl S4Vectors]; };
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GenomicAlignments = derive2 { name="GenomicAlignments"; version="1.32.0"; sha256="1ifmlc0488f5yzcf4p92dmdc7psxl5c0aa7qpxjk0a07gf7lldbi"; depends=[BiocGenerics BiocParallel Biostrings GenomeInfoDb GenomicRanges IRanges Rsamtools S4Vectors SummarizedExperiment]; };
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GenomicDataCommons = derive2 { name="GenomicDataCommons"; version="1.20.1"; sha256="0w275sn7sr2c3z3w00klj9w7ks7x3xqi7rvb8r19yyz481kd0z54"; depends=[dplyr GenomicRanges httr IRanges jsonlite magrittr rappdirs readr rlang tibble xml2]; };
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GenomicDistributions = derive2 { name="GenomicDistributions"; version="1.4.1"; sha256="1b9jgwaivk6xmd97qrb0wb39dwmf4x2d7zd3q428k7wrkrk4cffw"; depends=[Biostrings broom data_table dplyr GenomeInfoDb GenomicRanges ggplot2 IRanges plyr reshape2 scales]; };
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GenomicFeatures = derive2 { name="GenomicFeatures"; version="1.48.0"; sha256="11j5xv6l877hcd16yyrgr1rf788d99dc1qw9pxbi4rh0bhsqfrdq"; depends=[AnnotationDbi Biobase BiocGenerics BiocIO biomaRt Biostrings DBI GenomeInfoDb GenomicRanges IRanges RCurl RSQLite rtracklayer S4Vectors XVector]; };
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GenomicFiles = derive2 { name="GenomicFiles"; version="1.32.0"; sha256="0qgpwz7296fqqnvk9fssn9cc738q2mqla34zwxpkr2xscfpyz93f"; depends=[BiocGenerics BiocParallel GenomeInfoDb GenomicAlignments GenomicRanges IRanges MatrixGenerics Rsamtools rtracklayer S4Vectors SummarizedExperiment VariantAnnotation]; };
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GenomicFeatures = derive2 { name="GenomicFeatures"; version="1.48.3"; sha256="0f14p1ma2y8l60p9sxmh5j0axws9by1cznczb2jxipphpb4slpl1"; depends=[AnnotationDbi Biobase BiocGenerics BiocIO biomaRt Biostrings DBI GenomeInfoDb GenomicRanges IRanges RCurl RSQLite rtracklayer S4Vectors XVector]; };
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GenomicFiles = derive2 { name="GenomicFiles"; version="1.32.1"; sha256="06ycfna26klx27vvsnlpgv46bymfrc8z0zkpag7nm4m23153ivkz"; depends=[BiocGenerics BiocParallel GenomeInfoDb GenomicAlignments GenomicRanges IRanges MatrixGenerics Rsamtools rtracklayer S4Vectors SummarizedExperiment VariantAnnotation]; };
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GenomicInteractionNodes = derive2 { name="GenomicInteractionNodes"; version="1.0.0"; sha256="064mvbgrhf098pyqabqdi70yskri5pa3fd1yylzwmabx3g7wvsw8"; depends=[AnnotationDbi GenomeInfoDb GenomicFeatures GenomicRanges GO_db graph IRanges RBGL S4Vectors]; };
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GenomicInteractions = derive2 { name="GenomicInteractions"; version="1.30.0"; sha256="0aph1hja5vfprxs3jl4zd1inhvih6m3v1p3jkm6w7xpj3jzvmgbx"; depends=[Biobase BiocGenerics data_table dplyr GenomeInfoDb GenomicRanges ggplot2 gridExtra Gviz igraph InteractionSet IRanges Rsamtools rtracklayer S4Vectors stringr]; };
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GenomicOZone = derive2 { name="GenomicOZone"; version="1.10.0"; sha256="1dhrlibbs41rl97rspnn4sc77ic5rv7l23vgm4qmgq37lv1crpdk"; depends=[biomaRt Ckmeans_1d_dp GenomeInfoDb GenomicRanges ggbio ggplot2 gridExtra IRanges lsr plyr Rdpack S4Vectors]; };
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GenomicRanges = derive2 { name="GenomicRanges"; version="1.48.0"; sha256="088rv1aclwq265pdg4hmks73nl0125vk0vigyi44n3djkrdx48yn"; depends=[BiocGenerics GenomeInfoDb IRanges S4Vectors XVector]; };
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GenomicScores = derive2 { name="GenomicScores"; version="2.8.0"; sha256="0zq9k4189dlc14f9rknsc1ffhpjzb2f4fzdaszfdbnd4rr43b79i"; depends=[AnnotationHub Biobase BiocFileCache BiocGenerics BiocManager Biostrings DelayedArray GenomeInfoDb GenomicRanges HDF5Array IRanges rhdf5 S4Vectors XML]; };
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GenomicScores = derive2 { name="GenomicScores"; version="2.8.2"; sha256="12rcxw69an1d5q7ar58xy8s871l47imw2nm08j054ivxslx8597j"; depends=[AnnotationHub Biobase BiocFileCache BiocGenerics BiocManager Biostrings DelayedArray GenomeInfoDb GenomicRanges HDF5Array httr IRanges rhdf5 S4Vectors XML]; };
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GenomicSuperSignature = derive2 { name="GenomicSuperSignature"; version="1.4.0"; sha256="09hfb3j1v4b2as4vwy87h5jqi4kzz179k4lzvw4csr0yvs80f3ks"; depends=[Biobase BiocFileCache ComplexHeatmap dplyr flextable ggplot2 ggpubr plotly S4Vectors SummarizedExperiment]; };
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GenomicTuples = derive2 { name="GenomicTuples"; version="1.30.0"; sha256="0mjw7vvw28lgb7yrsymnixambnwasq79hfbcc3rw24c0srad6hsw"; depends=[BiocGenerics data_table GenomeInfoDb GenomicRanges IRanges Rcpp S4Vectors]; };
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GeoDiff = derive2 { name="GeoDiff"; version="1.2.0"; sha256="0s0bcx6j7varibkv5gwf29kld8znzz0dlbsrip6qxg5w23wwdhcz"; depends=[Biobase GeomxTools lme4 Matrix NanoStringNCTools plyr Rcpp RcppArmadillo robust roptim testthat withr]; };
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@ -442,10 +442,10 @@ in with self; {
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GraphAT = derive2 { name="GraphAT"; version="1.68.0"; sha256="1s5qcykfprqwqbhmlp64yxmjaxskwrxgh93j4idzgp71md1k5sf1"; depends=[graph MCMCpack]; };
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GraphAlignment = derive2 { name="GraphAlignment"; version="1.60.0"; sha256="0spjsqb8rx6si5lshk0drlq1h4h5jgb6bmcwdh0wz9755npz0p8m"; depends=[]; };
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GraphPAC = derive2 { name="GraphPAC"; version="1.38.0"; sha256="1qrcxcb68bx1kzpilrd61m14902wl490kmzkjj9bv35w20ln1f3h"; depends=[igraph iPAC RMallow TSP]; };
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GreyListChIP = derive2 { name="GreyListChIP"; version="1.28.0"; sha256="1ix1lfnj1ayh8knq0d1cz1nrwkcrnpbsbymgip1n7yisjyw801wb"; depends=[BSgenome GenomeInfoDb GenomicAlignments GenomicRanges MASS Rsamtools rtracklayer SummarizedExperiment]; };
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GreyListChIP = derive2 { name="GreyListChIP"; version="1.28.1"; sha256="0w52vwvjarql19bsv40b80yn701qx8c9d0clsjhj85wmzj2p6dhg"; depends=[BSgenome GenomeInfoDb GenomicAlignments GenomicRanges MASS Rsamtools rtracklayer SummarizedExperiment]; };
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Guitar = derive2 { name="Guitar"; version="2.12.0"; sha256="09grsasnnk7rmlzjh4lhas9r5spzcsrvmdqj6fx1dk22sckcqahh"; depends=[AnnotationDbi dplyr GenomicFeatures GenomicRanges ggplot2 knitr magrittr rtracklayer]; };
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Gviz = derive2 { name="Gviz"; version="1.40.1"; sha256="0as3sxhv21bqqrpvafcqim7798hhkzj3q40hy1rqyhv2lhj4rbvi"; depends=[AnnotationDbi Biobase BiocGenerics biomaRt Biostrings biovizBase BSgenome digest ensembldb GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges lattice latticeExtra matrixStats RColorBrewer Rsamtools rtracklayer S4Vectors XVector]; };
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HDF5Array = derive2 { name="HDF5Array"; version="1.24.0"; sha256="0s9vj74359ckmwl8r951jxrzkidslwdl9qamkhz8ilw8b5awxyw4"; depends=[BiocGenerics DelayedArray IRanges Matrix rhdf5 rhdf5filters Rhdf5lib S4Vectors]; };
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HDF5Array = derive2 { name="HDF5Array"; version="1.24.1"; sha256="1r1lg7k60qgb489xkypd4gvm1fmdlihvylb5va6xj58ipndbfday"; depends=[BiocGenerics DelayedArray IRanges Matrix rhdf5 rhdf5filters Rhdf5lib S4Vectors]; };
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HDTD = derive2 { name="HDTD"; version="1.30.0"; sha256="084bx1qwlibpd6xna29sb9nfksxa3z4jiz4l3fhkl8n5ww6k33pq"; depends=[Rcpp RcppArmadillo]; };
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HELP = derive2 { name="HELP"; version="1.54.0"; sha256="1sk3433d90msi6g0rpvsj8fdvr7isqs7gna409fcya2n4dlgmbs1"; depends=[Biobase]; };
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HEM = derive2 { name="HEM"; version="1.68.0"; sha256="1hq6i9rjrlis4fmi6zc06d37562vvv0sbsm4mihyrfmmn87k06wq"; depends=[Biobase]; };
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@ -465,7 +465,7 @@ in with self; {
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Heatplus = derive2 { name="Heatplus"; version="3.4.0"; sha256="0b1mzxysmrqinp93p587apna8p0llmawblwj93icydqxxm2jkhb1"; depends=[RColorBrewer]; };
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HelloRanges = derive2 { name="HelloRanges"; version="1.22.0"; sha256="1mmp19gpmpgn3kw9wjgsdc25hf4jfgg9bkjplg2qaf8rvm0mj8ih"; depends=[BiocGenerics BiocIO Biostrings BSgenome docopt GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges Rsamtools rtracklayer S4Vectors SummarizedExperiment VariantAnnotation]; };
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HiCBricks = derive2 { name="HiCBricks"; version="1.14.0"; sha256="0zf4mpq1bv7hhylrwnz3ia26mxwjyfx6rr9l9hxcjvm6zxh856dc"; depends=[BiocParallel curl data_table digest GenomeInfoDb GenomicRanges ggplot2 IRanges jsonlite R_utils R6 RColorBrewer readr reshape2 rhdf5 S4Vectors scales stringr tibble viridis]; };
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HiCDCPlus = derive2 { name="HiCDCPlus"; version="1.4.0"; sha256="1rxiv734c1mpm7xaad2iv8hbwliq1mjhqm48f54yfcr50w0k31yg"; depends=[bbmle Biostrings BSgenome data_table dplyr GenomeInfoDb GenomicInteractions GenomicRanges InteractionSet IRanges MASS pscl R_utils Rcpp rlang rtracklayer S4Vectors tibble tidyr]; };
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HiCDCPlus = derive2 { name="HiCDCPlus"; version="1.4.2"; sha256="0psww4sl4m5ynkv53xzyrigxzbypjdhqivg4r64993dlgcdsyi48"; depends=[bbmle Biostrings BSgenome data_table dplyr GenomeInfoDb GenomicInteractions GenomicRanges InteractionSet IRanges MASS pscl R_utils Rcpp rlang rtracklayer S4Vectors tibble tidyr]; };
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HiCcompare = derive2 { name="HiCcompare"; version="1.18.0"; sha256="0bgfa085x3w8g005iwnydv1c5i2sz12h5pksmki3427im6khycmr"; depends=[BiocParallel data_table dplyr GenomicRanges ggplot2 gridExtra gtools InteractionSet IRanges KernSmooth mgcv pheatmap QDNAseq rhdf5 S4Vectors]; };
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HiLDA = derive2 { name="HiLDA"; version="1.10.0"; sha256="0rf96isx2qwy7fs8y43bamfcdypiwbh5gggxqmdwdgkk0zhcpnls"; depends=[abind BiocGenerics Biostrings BSgenome_Hsapiens_UCSC_hg19 cowplot forcats GenomicFeatures GenomicRanges ggplot2 R2jags Rcpp S4Vectors stringr tidyr TxDb_Hsapiens_UCSC_hg19_knownGene XVector]; };
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HiTC = derive2 { name="HiTC"; version="1.40.0"; sha256="1pkshlrra26cad0hf8a54brlkazni6rsvrplh36azxapx5rpps4s"; depends=[Biostrings GenomeInfoDb GenomicRanges IRanges Matrix RColorBrewer rtracklayer]; };
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@ -487,7 +487,7 @@ in with self; {
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IPO = derive2 { name="IPO"; version="1.21.0"; sha256="1kf84n6af1aqq2lcm1yffc4kkdnjyc0lw9yjqvifhl03ba8kbmp0"; depends=[BiocParallel CAMERA rsm xcms]; };
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IRISFGM = derive2 { name="IRISFGM"; version="1.4.0"; sha256="13c9xk3gmqg0chzhmd6kj9fwmc11mc2j3wqin5202dkkn7x9b170"; depends=[AdaptGauss AnnotationDbi anocva clusterProfiler colorspace DEsingle DrImpute ggplot2 ggpubr ggraph igraph knitr Matrix MCL mixtools org_Hs_eg_db org_Mm_eg_db pheatmap Polychrome RColorBrewer Rcpp scater scran Seurat SingleCellExperiment]; };
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IRanges = derive2 { name="IRanges"; version="2.30.0"; sha256="0hfx5n0b4pqrrc1w2dik596803ly8ffnxfs768iy5l5kr8wwyc8k"; depends=[BiocGenerics S4Vectors]; };
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ISAnalytics = derive2 { name="ISAnalytics"; version="1.6.0"; sha256="0bqppw0j9sgy0c81cnidzji4089ybfad8y82pyrzpki04ga0zr37"; depends=[BiocParallel bslib data_table datamods dplyr forcats fs ggplot2 ggrepel glue lifecycle lubridate magrittr psych purrr Rcapture readr readxl rlang shiny shinyWidgets stringr tibble tidyr]; };
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ISAnalytics = derive2 { name="ISAnalytics"; version="1.6.2"; sha256="10arh47m7pg81rry1hb4pdfd0b5rdcj81lz9i32xlxanh3sp8kjv"; depends=[BiocParallel bslib data_table datamods dplyr forcats fs ggplot2 ggrepel glue lifecycle lubridate magrittr psych purrr Rcapture readr readxl rlang shiny shinyWidgets stringr tibble tidyr]; };
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ISoLDE = derive2 { name="ISoLDE"; version="1.24.0"; sha256="13cgy5hr4y6l3fkq2fx43wm4aypn5k3wp159kdqgp00lywd7pzxp"; depends=[]; };
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ITALICS = derive2 { name="ITALICS"; version="2.56.0"; sha256="150kfwhf47ipr2aql5cxli2hhs3cmgcya9aag0il41xy0wgc96k5"; depends=[affxparser DBI GLAD ITALICSData oligo oligoClasses pd_mapping50k_xba240]; };
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IVAS = derive2 { name="IVAS"; version="2.16.0"; sha256="1flsha57b7p2rnnrg4vs9dpghr9kf6g92r0xng3rrmxzb9i88kzw"; depends=[AnnotationDbi Biobase BiocGenerics BiocParallel doParallel foreach GenomeInfoDb GenomicFeatures GenomicRanges ggfortify ggplot2 IRanges lme4 Matrix S4Vectors]; };
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@ -511,7 +511,7 @@ in with self; {
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IsoformSwitchAnalyzeR = derive2 { name="IsoformSwitchAnalyzeR"; version="1.18.0"; sha256="0n1gb9azxa1mxpsqvw3i3kf72f45nyjj1kgwwrzhd88n3g63lvkd"; depends=[Biobase BiocGenerics Biostrings BSgenome DBI DEXSeq dplyr DRIMSeq edgeR futile_logger GenomeInfoDb GenomicRanges ggplot2 gridExtra IRanges limma magrittr plyr RColorBrewer RCurl readr reshape2 rtracklayer stringr tibble tximeta tximport VennDiagram XVector]; };
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KBoost = derive2 { name="KBoost"; version="1.4.0"; sha256="03rlkz6sblc6x2g1qy2n3di4gpribhxyivm2ddqsxzlm74f24mc1"; depends=[]; };
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KCsmart = derive2 { name="KCsmart"; version="2.54.0"; sha256="1qw4ag113rkg6lv556m0wv5c89r86f9sw1jzdg6mx4vrprnl64lv"; depends=[BiocGenerics KernSmooth multtest siggenes]; };
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KEGGREST = derive2 { name="KEGGREST"; version="1.36.0"; sha256="0hzlm6nzmx0iyjh063512a3ghc1xqb58g5z2bnd2wl4y42iww7bg"; depends=[Biostrings httr png]; };
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KEGGREST = derive2 { name="KEGGREST"; version="1.36.2"; sha256="1rn03w8y80prbvzahkvf8275haiymnjj1ijcgn55p3d0sb54yzgw"; depends=[Biostrings httr png]; };
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KEGGgraph = derive2 { name="KEGGgraph"; version="1.56.0"; sha256="15pq040pcg8hr18xixmjp59xb7mgvygjv6kisqk8yv99l1611ndx"; depends=[graph RCurl Rgraphviz XML]; };
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KEGGlincs = derive2 { name="KEGGlincs"; version="1.22.0"; sha256="1lrs6nqsfsafnvkyj46851r7m6b10dq8f6jfikqyhbv4cisw4kln"; depends=[AnnotationDbi gtools hgu133a_db httr igraph KEGGgraph KEGGREST KOdata org_Hs_eg_db plyr RJSONIO XML]; };
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KinSwingR = derive2 { name="KinSwingR"; version="1.14.0"; sha256="1703kfmgp52v6yd5pjj8d7s8j725xq4xgrzsi015jgrka76q1860"; depends=[BiocParallel data_table sqldf]; };
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@ -559,7 +559,7 @@ in with self; {
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MEB = derive2 { name="MEB"; version="1.10.0"; sha256="02zp4zk2986xajp91rak4pg8vwxp1f78wv3qwjmc8pig5m65a22j"; depends=[e1071 SummarizedExperiment]; };
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MEDIPS = derive2 { name="MEDIPS"; version="1.48.0"; sha256="1qxg2a7jqhnbn7zvlvn4i4kjg010ab34afds2sgcsvl4qpqcj9d0"; depends=[biomaRt Biostrings BSgenome DNAcopy edgeR GenomicRanges gtools IRanges preprocessCore Rsamtools rtracklayer]; };
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MEDME = derive2 { name="MEDME"; version="1.56.0"; sha256="0jfqr2bc8v45j38nmk9k03p02imvmrhfbd7b2gj9zcnbj4j3z6rz"; depends=[Biostrings drc MASS]; };
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MEIGOR = derive2 { name="MEIGOR"; version="1.29.0"; sha256="1rf9l25xdgpsb9845y4azi4gda4msh8mrv1qc0wply6lqp6w0aiq"; depends=[CNORode deSolve Rsolnp snowfall]; };
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MEIGOR = derive2 { name="MEIGOR"; version="1.30.0"; sha256="1qfb969jjm6xyrnq1l108mhjrgzm886aiakiacagsbivjcq7ianf"; depends=[CNORode deSolve Rsolnp snowfall]; };
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MGFM = derive2 { name="MGFM"; version="1.30.0"; sha256="0f0flpv2i6531k4vdkwljpzzljpdsyj32arf56q362vq0zpaf0k9"; depends=[annotate AnnotationDbi]; };
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MGFR = derive2 { name="MGFR"; version="1.22.0"; sha256="1v9aljss454kjqzrwzgfirqfpi59f36l9jgmfd8zwkljwgi8i6fn"; depends=[annotate biomaRt]; };
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MIGSA = derive2 { name="MIGSA"; version="1.20.0"; sha256="0ijf33z9xgqb67zhym0zn7jjfyh8kr7bvhm341b517r5igb311fb"; depends=[AnnotationDbi Biobase BiocGenerics BiocParallel data_table edgeR futile_logger ggdendro ggplot2 GO_db GOstats graph GSEABase ismev jsonlite limma matrixStats org_Hs_eg_db RBGL reshape2 Rgraphviz vegan]; };
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@ -570,7 +570,7 @@ in with self; {
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MLSeq = derive2 { name="MLSeq"; version="2.14.0"; sha256="0ajkxa6wm215df6i8y7z9ha68m25p5kg5hzk2ni4v07w6mn3cikj"; depends=[Biobase caret DESeq2 edgeR foreach ggplot2 limma pamr plyr sSeq SummarizedExperiment testthat VennDiagram xtable]; };
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MMAPPR2 = derive2 { name="MMAPPR2"; version="1.10.0"; sha256="1w8ajra7ip9yfmzinvdgxcm1n808saj0shfx0irflmz54a829kfr"; depends=[Biobase BiocGenerics BiocParallel data_table dplyr ensemblVEP GenomeInfoDb GenomicRanges gmapR IRanges magrittr Rsamtools S4Vectors stringr tidyr VariantAnnotation VariantTools]; };
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MMDiff2 = derive2 { name="MMDiff2"; version="1.24.0"; sha256="031d3j2d6rqj5adaflbhq1q40h1573mg44vxk07hg3ky6w55mv82"; depends=[Biobase Biostrings BSgenome GenomicRanges ggplot2 locfit RColorBrewer Rsamtools S4Vectors shiny]; };
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MMUPHin = derive2 { name="MMUPHin"; version="1.10.0"; sha256="1ljrlnbp12n4fkhnp4id1rvz790vigmrk3hlyk2nziv8vz5m6j41"; depends=[cowplot dplyr fpc ggplot2 igraph Maaslin2 metafor tidyr]; };
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MMUPHin = derive2 { name="MMUPHin"; version="1.10.1"; sha256="02xy8pm7yp77px5wklgj0dpsxal400lxphb341c2pq21n6j57s75"; depends=[cowplot dplyr fpc ggplot2 igraph Maaslin2 metafor tidyr]; };
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MODA = derive2 { name="MODA"; version="1.22.0"; sha256="1aa5g2zy251q3rpy83c4siyvdnrzw5cb3a136qrxd69z6pfpnkx3"; depends=[AMOUNTAIN cluster dynamicTreeCut igraph RColorBrewer WGCNA]; };
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MOFA2 = derive2 { name="MOFA2"; version="1.6.0"; sha256="1cdx2zgmicn5qa59x794mjcnz9csgmsscl21qd9yhwc5n9fj0zqw"; depends=[basilisk corrplot cowplot DelayedArray dplyr forcats ggplot2 ggrepel HDF5Array magrittr pheatmap RColorBrewer reshape2 reticulate rhdf5 Rtsne stringi tidyr uwot]; };
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MOGAMUN = derive2 { name="MOGAMUN"; version="1.6.0"; sha256="1wgpr6ci1hmzl1racszxfvgk95q5x4ca21rxhimimgag1gkk472b"; depends=[BiocParallel igraph RCy3 RUnit stringr]; };
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@ -583,7 +583,7 @@ in with self; {
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MSPrep = derive2 { name="MSPrep"; version="1.6.0"; sha256="1g0kd405iypvl0vkc190a1mm4gf17pdvk32ij3m23d03pz6qsdpg"; depends=[crmn dplyr magrittr missForest pcaMethods preprocessCore rlang S4Vectors stringr SummarizedExperiment sva tibble tidyr VIM]; };
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MSnID = derive2 { name="MSnID"; version="1.30.0"; sha256="1yiw95p40nz0pvq7s4i0xg02r9yqmnknak00z4lkw8jij3w3rkkq"; depends=[AnnotationDbi AnnotationHub Biobase BiocGenerics BiocStyle Biostrings data_table doParallel dplyr foreach ggplot2 iterators msmsTests MSnbase mzID mzR ProtGenerics purrr R_cache Rcpp reshape2 rlang RUnit stringr tibble xtable]; };
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MSnbase = derive2 { name="MSnbase"; version="2.22.0"; sha256="1xzn0k3c2wn6c6gv90hddy3c201sg927342zrw9ig2xap0r053x3"; depends=[affy Biobase BiocGenerics BiocParallel digest ggplot2 impute IRanges lattice MALDIquant MASS MsCoreUtils mzID mzR pcaMethods plyr ProtGenerics Rcpp S4Vectors scales vsn XML]; };
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MSstats = derive2 { name="MSstats"; version="4.4.0"; sha256="1mzqimqb9a0dqjyhna8fsibgzxilvj14vc2vq55pq4px8k0n5jdl"; depends=[checkmate data_table ggplot2 ggrepel gplots limma lme4 marray MASS MSstatsConvert preprocessCore Rcpp RcppArmadillo survival]; };
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MSstats = derive2 { name="MSstats"; version="4.4.1"; sha256="0n03spd9a57wqsl3hmz5flsh8ijzgykg2iv7f05n0a7iwrq75ms4"; depends=[checkmate data_table ggplot2 ggrepel gplots limma lme4 marray MASS MSstatsConvert preprocessCore Rcpp RcppArmadillo survival]; };
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MSstatsConvert = derive2 { name="MSstatsConvert"; version="1.6.0"; sha256="01rh07a5ibk3fn7dvmmj4665xki03jvlybv40sa0fzf25z07nsfg"; depends=[checkmate data_table log4r stringi]; };
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MSstatsLOBD = derive2 { name="MSstatsLOBD"; version="1.4.0"; sha256="177fz522fx2bph66gm945jrg5wvr7cz98n0wbn7ndym85v6dql32"; depends=[ggplot2 minpack_lm Rcpp]; };
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MSstatsLiP = derive2 { name="MSstatsLiP"; version="1.2.1"; sha256="1yx686wk5ykl31qq3fxcsvh8bw5hrv3yiqrkc1jngxjph1xzx2bg"; depends=[Biostrings checkmate data_table dplyr factoextra ggplot2 ggpubr gridExtra MSstats MSstatsConvert MSstatsPTM purrr Rcpp scales stringr tibble tidyr tidyverse]; };
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@ -616,7 +616,7 @@ in with self; {
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Metab = derive2 { name="Metab"; version="1.30.0"; sha256="1hy9h8q61did3j3md72gdjsnxv6x7vgkqidaffn8c66xcbc98pw5"; depends=[pander svDialogs xcms]; };
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MetaboAnnotation = derive2 { name="MetaboAnnotation"; version="1.0.0"; sha256="08xdp7s5c4xb9qhg91mgyb07d21l327bjyqzvrnwbn8ynkqyv3wh"; depends=[BiocGenerics BiocParallel MetaboCoreUtils MsCoreUtils ProtGenerics QFeatures S4Vectors Spectra SummarizedExperiment]; };
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MetaboCoreUtils = derive2 { name="MetaboCoreUtils"; version="1.4.0"; sha256="0lvc8hzn0czzrz01hwkkhrsshq5k5nikc5irn6hbi3sv93r2bzka"; depends=[MsCoreUtils]; };
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MetaboSignal = derive2 { name="MetaboSignal"; version="1.26.0"; sha256="03gcz41mzlkgr12krswvav1wbwv3hxvqrzkgamvriq8rq80q2pdc"; depends=[AnnotationDbi biomaRt EnsDb_Hsapiens_v75 hpar igraph KEGGgraph KEGGREST MWASTools mygene org_Hs_eg_db RCurl]; };
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MetaboSignal = derive2 { name="MetaboSignal"; version="1.26.1"; sha256="1wmgwslzr9j42vcvv5mafz472bbqfd9n9j7pcr9ddjzfhczq02df"; depends=[AnnotationDbi biomaRt EnsDb_Hsapiens_v75 hpar igraph KEGGgraph KEGGREST MWASTools mygene org_Hs_eg_db RCurl]; };
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MethPed = derive2 { name="MethPed"; version="1.24.0"; sha256="145pm17h164qqj4vhdrgrqqj5j1axls0841c6ikz5yp0l13065ij"; depends=[Biobase randomForest]; };
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MethReg = derive2 { name="MethReg"; version="1.6.0"; sha256="1133ndj4q6ddmq6rjjljj8f01zrh5rn09pgj6g0yp4yfpymbkj04"; depends=[AnnotationHub DelayedArray dplyr ExperimentHub GenomicRanges ggplot2 ggpubr IRanges MASS Matrix plyr progress pscl readr rlang S4Vectors sesame sesameData sfsmisc stringr SummarizedExperiment tibble tidyr]; };
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MethTargetedNGS = derive2 { name="MethTargetedNGS"; version="1.28.0"; sha256="06cvyic6y1g6j397j9xvsqhjhwlarldxqfg28i00ym6l6hzcad4l"; depends=[Biostrings gplots seqinr stringr]; };
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@ -628,7 +628,7 @@ in with self; {
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MiPP = derive2 { name="MiPP"; version="1.68.0"; sha256="080cc1y32yi046xsj05vppp1l3c2sdyjclw8p439kmakcrf0sigf"; depends=[Biobase e1071 MASS]; };
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MiRaGE = derive2 { name="MiRaGE"; version="1.38.0"; sha256="0w4c41izigparfaddj5ffccxw7v33gc11zh0b1cdyz2hacmw03ly"; depends=[AnnotationDbi Biobase BiocGenerics BiocManager S4Vectors]; };
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MicrobiomeProfiler = derive2 { name="MicrobiomeProfiler"; version="1.2.0"; sha256="0czli81lqbx1xkhj5yqlixjgszk4whvckhjpw9k70ggcx9svc249"; depends=[clusterProfiler config DT enrichplot ggplot2 golem htmltools magrittr shiny shinycustomloader shinyWidgets]; };
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MicrobiotaProcess = derive2 { name="MicrobiotaProcess"; version="1.8.0"; sha256="18x5dic3g60irn5xqn7hn84kfnyfm9yi9a033366k8wfws6sixpm"; depends=[ape Biostrings coin dplyr dtplyr foreach ggplot2 ggrepel ggsignif ggstar ggtree ggtreeExtra magrittr MASS patchwork pillar rlang SummarizedExperiment tibble tidyr tidyselect tidytree treeio vegan zoo]; };
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MicrobiotaProcess = derive2 { name="MicrobiotaProcess"; version="1.8.1"; sha256="0gv5vkrrp4lk9df2brjacqa313h78wayzal63d5mmszjfg9cd7s3"; depends=[ape Biostrings coin dplyr dtplyr foreach ggplot2 ggrepel ggsignif ggstar ggtree ggtreeExtra magrittr MASS patchwork pillar plyr rlang SummarizedExperiment tibble tidyr tidyselect tidytree treeio vegan zoo]; };
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MineICA = derive2 { name="MineICA"; version="1.36.0"; sha256="0lwpykysp8arq6rhfq9w6w5phxmj41lk8xg473b2n4pcfc6sh34h"; depends=[annotate AnnotationDbi Biobase BiocGenerics biomaRt cluster colorspace fastICA foreach fpc ggplot2 GOstats graph gtools Hmisc igraph JADE lumi lumiHumanAll_db marray mclust plyr RColorBrewer Rgraphviz scales xtable]; };
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MinimumDistance = derive2 { name="MinimumDistance"; version="1.40.0"; sha256="0409nqlhjnx0l8zcy71zrawjbml1rmjkgch9a87zcc1j2phnpdch"; depends=[Biobase BiocGenerics data_table DNAcopy ff foreach GenomeInfoDb GenomicRanges IRanges lattice MatrixGenerics matrixStats oligoClasses S4Vectors SummarizedExperiment VanillaICE]; };
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MobilityTransformR = derive2 { name="MobilityTransformR"; version="1.0.0"; sha256="0x3xxh54sdlb6dan9rrrg116vfr1q4b0z9fdjaqh52qbwchy1x82"; depends=[MetaboCoreUtils MSnbase Spectra xcms]; };
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@ -650,11 +650,11 @@ in with self; {
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MultiBaC = derive2 { name="MultiBaC"; version="1.6.0"; sha256="028jc5kr84qi9m38g6xqf7cizif2qzg2j4ypvyav7syqb9n0927s"; depends=[ggplot2 Matrix MultiAssayExperiment pcaMethods plotrix ropls]; };
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MultiDataSet = derive2 { name="MultiDataSet"; version="1.24.0"; sha256="0rfs6jkzh1i4mj1pgfk4lwzmcl8pcwizra3q3282x3d8h2g98qnf"; depends=[Biobase BiocGenerics GenomicRanges ggplot2 ggrepel IRanges limma qqman S4Vectors SummarizedExperiment]; };
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MultiMed = derive2 { name="MultiMed"; version="2.18.0"; sha256="1cdkkspmwn67d685kgna8fr9w3mqrzg6qbv6vzr81knrwmhgxp1z"; depends=[]; };
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MungeSumstats = derive2 { name="MungeSumstats"; version="1.4.0"; sha256="1wypz2q6f6kijsnp508xljkma4kwb2gyzs6p6ci3s99amx901z96"; depends=[Biostrings BSgenome data_table dplyr GenomeInfoDb GenomicRanges googleAuthR httr jsonlite magrittr R_utils RCurl rtracklayer stringr VariantAnnotation]; };
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MungeSumstats = derive2 { name="MungeSumstats"; version="1.4.5"; sha256="14c8gx5pjppf7z0dcwdrg6cmbwg7k7k4782a13v47xiwhpxszxd2"; depends=[Biostrings BSgenome data_table dplyr GenomeInfoDb GenomicRanges googleAuthR httr IRanges jsonlite magrittr R_utils RCurl rtracklayer VariantAnnotation]; };
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MutationalPatterns = derive2 { name="MutationalPatterns"; version="3.6.0"; sha256="113b2hrc0n47qz144xhky93jcm6qh6flzadq5y0plga5jrz0rnwg"; depends=[BiocGenerics Biostrings BSgenome cowplot dplyr GenomeInfoDb GenomicRanges ggalluvial ggdendro ggplot2 IRanges magrittr NMF pracma purrr RColorBrewer S4Vectors stringr tibble tidyr VariantAnnotation]; };
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NADfinder = derive2 { name="NADfinder"; version="1.20.0"; sha256="0ynwf5ij694a46qa2fl4xvvxalh8a9mh6k0gxd3dfbi692lm6ihv"; depends=[ATACseqQC baseline BiocGenerics corrplot csaw EmpiricalBrownsMethod GenomeInfoDb GenomicAlignments GenomicRanges IRanges limma metap Rsamtools rtracklayer S4Vectors signal SummarizedExperiment trackViewer]; };
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NBAMSeq = derive2 { name="NBAMSeq"; version="1.12.0"; sha256="0rgyhijlv7knnb5z2zswxdicyblrxrnyliw1hlppdwsjwjyd3ixj"; depends=[BiocParallel DESeq2 genefilter mgcv S4Vectors SummarizedExperiment]; };
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NBSplice = derive2 { name="NBSplice"; version="1.14.0"; sha256="1hkcjn1icc6rmg13gnkya6xsmxa71pggdc9fzg8i47bs4cw0y6fb"; depends=[BiocParallel car edgeR ggplot2 MASS mppa reshape2]; };
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NBSplice = derive2 { name="NBSplice"; version="1.14.0"; sha256="1hkcjn1icc6rmg13gnkya6xsmxa71pggdc9fzg8i47bs4cw0y6fb"; depends=[BiocParallel car edgeR ggplot2 MASS reshape2]; };
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NCIgraph = derive2 { name="NCIgraph"; version="1.44.0"; sha256="15srh42yrax35kkxiansx9aabraifyh70dxv17fg0vkf9pdndxic"; depends=[graph KEGGgraph R_methodsS3 RBGL RCy3]; };
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NOISeq = derive2 { name="NOISeq"; version="2.40.0"; sha256="0ah6adlhv4254jkssinn2ik8n811hd1nw85bnzqk2kwhl49nrk27"; depends=[Biobase Matrix]; };
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NPARC = derive2 { name="NPARC"; version="1.8.0"; sha256="1c9zi2a3jki589brg09hzmlzqxzlnq2xwd1674v0vrc70d99ybs9"; depends=[BiocParallel broom dplyr magrittr MASS rlang tidyr]; };
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@ -674,11 +674,11 @@ in with self; {
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NormalyzerDE = derive2 { name="NormalyzerDE"; version="1.14.0"; sha256="13z5vgnmx6d85ygb1hj3s24mq4jcnfhx6pgigi9ha73p8rimixs8"; depends=[ape Biobase car ggforce ggplot2 limma MASS matrixStats preprocessCore raster RcmdrMisc SummarizedExperiment vsn]; };
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NormqPCR = derive2 { name="NormqPCR"; version="1.42.0"; sha256="1jrif7cqippczyzf3nszbwxn0a58fvlmkcwb9as0ymv9qvh372vx"; depends=[Biobase qpcR RColorBrewer ReadqPCR]; };
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NuPoP = derive2 { name="NuPoP"; version="2.4.0"; sha256="0gxanqk1xarjgnczll3fj48hx0b7iizkixy8z94d3q28y5zcqvfz"; depends=[]; };
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NxtIRFcore = derive2 { name="NxtIRFcore"; version="1.2.0"; sha256="0qvv2yp6y9aylmhv9y640xqqx47ck5gazwnki4x5fwgb0f5v0jc0"; depends=[AnnotationHub BiocFileCache BiocGenerics BiocParallel Biostrings BSgenome data_table DelayedArray DelayedMatrixStats fst genefilter GenomeInfoDb GenomicRanges ggplot2 HDF5Array IRanges magrittr NxtIRFdata plotly R_utils Rcpp RcppProgress rhdf5 rtracklayer S4Vectors SummarizedExperiment zlibbioc]; };
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NxtIRFcore = derive2 { name="NxtIRFcore"; version="1.2.1"; sha256="1mjd09ywdsmzn46qgh3gzalvid3d9b6wajwkj8siibx7rpmc0rwz"; depends=[AnnotationHub BiocFileCache BiocGenerics BiocParallel Biostrings BSgenome data_table DelayedArray DelayedMatrixStats fst genefilter GenomeInfoDb GenomicRanges ggplot2 HDF5Array IRanges magrittr NxtIRFdata plotly R_utils Rcpp RcppProgress rhdf5 rtracklayer S4Vectors SummarizedExperiment zlibbioc]; };
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OCplus = derive2 { name="OCplus"; version="1.70.0"; sha256="0smrb7k510x19pgpk53xl6c8gc8bccasg6d461jwzblx01mm4l2x"; depends=[akima multtest]; };
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ODER = derive2 { name="ODER"; version="1.2.0"; sha256="1vj3l4032sbjmbi508lzhl41gr3wpyma2ch8fm7arv5csksnn20s"; depends=[BiocFileCache BiocGenerics dasper data_table derfinder dplyr GenomeInfoDb GenomicRanges ggplot2 ggpubr ggrepel IRanges magrittr megadepth plyr purrr rtracklayer S4Vectors stringr tibble]; };
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OGRE = derive2 { name="OGRE"; version="1.0.0"; sha256="1lm6hqi9lc5xpdgbvwcjzhcjw7qp2ympi7w17s90mmki0g36rf6x"; depends=[AnnotationHub assertthat data_table DT GenomeInfoDb GenomicRanges ggplot2 Gviz IRanges rtracklayer S4Vectors shiny shinyBS shinydashboard shinyFiles tidyr]; };
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OLIN = derive2 { name="OLIN"; version="1.73.0"; sha256="0569hcy2rs6bw7z62cmldz07193p2wbm3yisgmihvq44b3q4saj1"; depends=[limma locfit marray]; };
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OLIN = derive2 { name="OLIN"; version="1.74.1"; sha256="0yv767qf9h6d9hyzlpwq2y5l874gyfn9mvrs8m5kjvzspnm6sisk"; depends=[limma locfit marray]; };
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OLINgui = derive2 { name="OLINgui"; version="1.70.0"; sha256="0pdnxp9i08faljafy91kxg7xiv9b2fh3k5c3gqdfrvwggx3d839x"; depends=[marray OLIN tkWidgets widgetTools]; };
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OMICsPCA = derive2 { name="OMICsPCA"; version="1.14.0"; sha256="0fldppwhjijw53s6q44g92n59pfmlz5049qsmna7nzqdh06l8wh6"; depends=[cluster clValid corrplot cowplot data_table factoextra FactoMineR fpc GenomeInfoDb ggplot2 HelloRanges IRanges kableExtra magick MASS MultiAssayExperiment NbClust OMICsPCAdata pdftools PerformanceAnalytics reshape2 rgl rmarkdown rtracklayer tidyr]; };
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OPWeight = derive2 { name="OPWeight"; version="1.18.0"; sha256="1k4qfbg29lll9hpkzbcbhfipyjn4rdpfyhm2wmr8a9jcp04fpl43"; depends=[MASS qvalue tibble]; };
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@ -698,7 +698,7 @@ in with self; {
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OpenStats = derive2 { name="OpenStats"; version="1.8.0"; sha256="08r2id3f6gx5s1va4gr6m191c9y44m2c6s5lbxr8xhrnpi4c61p0"; depends=[AICcmodavg car Hmisc jsonlite knitr MASS nlme rlist summarytools]; };
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OrderedList = derive2 { name="OrderedList"; version="1.68.0"; sha256="15085hiyqn5ci5ahc674hp1j2lszdm6gm8acs1b87rg6pp5zjl4q"; depends=[Biobase twilight]; };
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Organism_dplyr = derive2 { name="Organism.dplyr"; version="1.24.0"; sha256="0j29f85d66c45ww3417xx376vpz0mmvga5n7h2cl1sd4h70b55as"; depends=[AnnotationDbi AnnotationFilter BiocFileCache DBI dbplyr dplyr GenomeInfoDb GenomicFeatures GenomicRanges IRanges rlang RSQLite S4Vectors tibble]; };
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OrganismDbi = derive2 { name="OrganismDbi"; version="1.38.0"; sha256="1xklaiyd4mv9sf9211flq1s68fhdn53y2i4l1k2ib39a4l6y9cyr"; depends=[AnnotationDbi Biobase BiocGenerics BiocManager DBI GenomicFeatures GenomicRanges graph IRanges RBGL S4Vectors]; };
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OrganismDbi = derive2 { name="OrganismDbi"; version="1.38.1"; sha256="0mxnxj8x4hc21psz39mf7qwvh1fsn6qyjgl5qffk1xxmasf69619"; depends=[AnnotationDbi Biobase BiocGenerics BiocManager DBI GenomicFeatures GenomicRanges graph IRanges RBGL S4Vectors]; };
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Oscope = derive2 { name="Oscope"; version="1.26.0"; sha256="0rbz82k96k7d8nrbcr8mnz24kq8x95yw7m55vg64i66gm5gks168"; depends=[BiocParallel cluster EBSeq testthat]; };
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PAA = derive2 { name="PAA"; version="1.30.0"; sha256="0nq79hwinz95f0rifpk18r26vfvymns8dvib0mx4jjd13k75xgzz"; depends=[e1071 gplots gtools limma MASS mRMRe randomForest Rcpp ROCR sva]; };
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PADOG = derive2 { name="PADOG"; version="1.38.0"; sha256="156w598w39gf1mc4jm0p7c7hip4vlsms7jvb3dj5h789bgr0whnq"; depends=[AnnotationDbi Biobase doRNG foreach GSA hgu133a_db hgu133plus2_db KEGGdzPathwaysGEO KEGGREST limma nlme]; };
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@ -726,18 +726,18 @@ in with self; {
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PSICQUIC = derive2 { name="PSICQUIC"; version="1.34.0"; sha256="0gkkxxbc2a7cin92qwn1masqfigyz9s4fhyy2daa17r3ckk4ccgx"; depends=[BiocGenerics biomaRt httr IRanges plyr RCurl]; };
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PSMatch = derive2 { name="PSMatch"; version="1.0.0"; sha256="027r2r70n9v54m6kww6bzaqvf7ahn42vh7fdbbb4m6xzbl62frmq"; depends=[BiocGenerics BiocParallel igraph Matrix MsCoreUtils ProtGenerics QFeatures S4Vectors]; };
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PWMEnrich = derive2 { name="PWMEnrich"; version="4.32.0"; sha256="031j563jcaakiasx1r8aflhqm0vq7j5628f9bv4kkyi5rhr3aix9"; depends=[BiocGenerics Biostrings evd gdata S4Vectors seqLogo]; };
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PanomiR = derive2 { name="PanomiR"; version="1.0.0"; sha256="0j5x7v2wz88bx1prhzxhj71jrwk5f72zm2kafh4h4lp77fgy8nhh"; depends=[clusterProfiler dplyr forcats GSEABase igraph limma metap org_Hs_eg_db preprocessCore RColorBrewer rlang tibble withr]; };
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PanomiR = derive2 { name="PanomiR"; version="1.0.1"; sha256="18cy3qxismfvb1r7ln386s84r81zl8z20zbam343dh1pzw7ll61y"; depends=[clusterProfiler dplyr forcats GSEABase igraph limma metap org_Hs_eg_db preprocessCore RColorBrewer rlang tibble withr]; };
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Path2PPI = derive2 { name="Path2PPI"; version="1.26.0"; sha256="0csqciqavnamyhsf7hx5c6x3ranr1h8wskzz09hf7rw65gxbn6jp"; depends=[igraph]; };
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PathNet = derive2 { name="PathNet"; version="1.36.0"; sha256="1xbwzvbnjgxby7xwgpl20qnx172lpzhm5z8rm3q1n3ww0n4z7pfk"; depends=[]; };
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PathoStat = derive2 { name="PathoStat"; version="1.22.0"; sha256="1f01vrncrw50jcvaivgqpjyc6h0ccphzifcw1aq03w39nrw55mz9"; depends=[ape BiocStyle ComplexHeatmap corpcor DESeq2 devtools dplyr DT edgeR ggplot2 glmnet gmodels knitr limma matrixStats phyloseq plotly plyr RColorBrewer rentrez reshape2 ROCR scales shiny shinyjs tidyr vegan webshot XML]; };
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PeacoQC = derive2 { name="PeacoQC"; version="1.6.0"; sha256="1b2jhph8nhx9iqia6cbs84aaz7srm7fchn7r0d55fmfnzg5cdr7z"; depends=[circlize ComplexHeatmap flowCore flowWorkspace ggplot2 gridExtra plyr]; };
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PepsNMR = derive2 { name="PepsNMR"; version="1.14.0"; sha256="04q4xminxkqzc88dqyrpddzdmcnj1n4ssspk3wnraplwrxhg1kcx"; depends=[ggplot2 gridExtra Matrix matrixStats ptw reshape2]; };
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PhIPData = derive2 { name="PhIPData"; version="1.4.0"; sha256="06fc0h2jn2v6n921rmxb37rdkk60v9il9x32w1ky2n5xaiqhx3yl"; depends=[BiocFileCache BiocGenerics cli edgeR GenomicRanges IRanges S4Vectors SummarizedExperiment]; };
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PharmacoGx = derive2 { name="PharmacoGx"; version="3.0.0"; sha256="0d52zbdis7ral6ds5fkwx68d7cigwngswcx53ij3np1n9wxihrqb"; depends=[Biobase BiocGenerics BiocParallel boot caTools checkmate coop CoreGx data_table downloader ggplot2 jsonlite magicaxis MultiAssayExperiment RColorBrewer Rcpp reshape2 S4Vectors SummarizedExperiment]; };
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PharmacoGx = derive2 { name="PharmacoGx"; version="3.0.2"; sha256="16mpqz4amzydwihniwz7ivj8z9lb0z9rmldk3j4f2f8gy49l63pi"; depends=[Biobase BiocGenerics BiocParallel boot caTools checkmate coop CoreGx data_table downloader ggplot2 jsonlite magicaxis MultiAssayExperiment RColorBrewer Rcpp reshape2 S4Vectors SummarizedExperiment]; };
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PhenStat = derive2 { name="PhenStat"; version="2.32.0"; sha256="1g8g7452vkl06vphmmb7vv090dng58cx9v3d1vhsxsf6bzqny4ql"; depends=[car corrplot ggplot2 graph knitr lme4 logistf MASS msgps nlme nortest pingr reshape SmoothWin]; };
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PhenoGeneRanker = derive2 { name="PhenoGeneRanker"; version="1.4.0"; sha256="0wzf9c3iimcq8hc78ai188slbhkgzq94nmzcd4gxzlgmk44524ap"; depends=[doParallel dplyr foreach igraph Matrix]; };
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PhosR = derive2 { name="PhosR"; version="1.6.0"; sha256="0rgqr458m5hbai1jmcxv73ay74bgd44iwjz98b848qgx4imz8jp2"; depends=[BiocGenerics circlize dendextend dplyr e1071 GGally ggdendro ggplot2 ggpubr ggtext igraph limma network pcaMethods pheatmap preprocessCore RColorBrewer reshape2 rlang ruv S4Vectors SummarizedExperiment tidyr]; };
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PhyloProfile = derive2 { name="PhyloProfile"; version="1.10.1"; sha256="1fgdszy6f7iy0rzkc72mqy9nv26whq1gsx39b12gkcr3h05imihp"; depends=[ape BiocStyle bioDist Biostrings colourpicker data_table DT energy ExperimentHub ggplot2 gridExtra OmaDB pbapply plyr RColorBrewer RCurl shiny shinyBS shinyFiles shinyjs xml2 yaml zoo]; };
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PhyloProfile = derive2 { name="PhyloProfile"; version="1.10.4"; sha256="07yivp5plcxzqp6rffghxl6m9if7h260wbylwfdrjyn86fxn15q1"; depends=[ape BiocStyle bioDist Biostrings colourpicker data_table DT energy ExperimentHub ggplot2 gridExtra OmaDB pbapply plyr RColorBrewer RCurl shiny shinyBS shinyFiles shinyjs xml2 yaml zoo]; };
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Pi = derive2 { name="Pi"; version="2.8.0"; sha256="0vpvpq7ss4x6qcz525zl71ysfh65zcqp13qym03s0v6r491gndnv"; depends=[BiocGenerics caret dnet dplyr GenomeInfoDb GenomicRanges ggnetwork ggplot2 ggrepel glmnet igraph IRanges lattice MASS Matrix osfr plot3D purrr randomForest RCircos readr ROCR scales supraHex tibble tidyr]; };
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Pigengene = derive2 { name="Pigengene"; version="1.22.0"; sha256="11bx3ivzfzh0bnmz77psz4vah0gm0vaa7pwbbkwjcra85sbzyxiz"; depends=[BiocStyle bnlearn C50 clusterProfiler DBI DOSE dplyr gdata ggplot2 GO_db graph impute MASS matrixStats openxlsx partykit pheatmap preprocessCore ReactomePA Rgraphviz WGCNA]; };
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PloGO2 = derive2 { name="PloGO2"; version="1.8.0"; sha256="1fwzim2x1yrd8jqbjg3zjnq8rpva7xnywsqmbab6cplx0qdy185s"; depends=[GO_db GOstats httr lattice openxlsx xtable]; };
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@ -745,7 +745,7 @@ in with self; {
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PoTRA = derive2 { name="PoTRA"; version="1.12.0"; sha256="0k93zj0mfs8pkr5cnf2y7bg9ynnwwr1acylsav8dcyz8vkc9r25k"; depends=[BiocGenerics graph graphite igraph org_Hs_eg_db]; };
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PrInCE = derive2 { name="PrInCE"; version="1.12.0"; sha256="02vnpdmns14g0qhizpify2p4mzkacj31ar31jmbxzg3bcbq2nz84"; depends=[Biobase dplyr forecast Hmisc LiblineaR magrittr MSnbase naivebayes progress purrr ranger Rdpack robustbase speedglm tester tidyr]; };
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PrecisionTrialDrawer = derive2 { name="PrecisionTrialDrawer"; version="1.11.0"; sha256="1miw8rj1zn1xv97dkgs66k9g21i6gp3j2m1l1akysskczgam3i2c"; depends=[BiocParallel biomaRt brglm data_table DT GenomicRanges ggplot2 ggrepel googleVis httr IRanges jsonlite LowMACAAnnotation magrittr matrixStats RColorBrewer reshape2 S4Vectors shiny shinyBS stringr XML]; };
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Prostar = derive2 { name="Prostar"; version="1.28.0"; sha256="1av29wvikn94yw2lc4d7i3j1fyyf5s5halp54m54l4dfs5c3b920"; depends=[colourpicker DAPAR DAPARdata data_table DT future highcharter htmlwidgets later promises R_utils rhandsontable sass shiny shinyAce shinyBS shinycssloaders shinyjqui shinyjs shinythemes shinyWidgets tibble webshot XML]; };
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Prostar = derive2 { name="Prostar"; version="1.28.1"; sha256="1gd6shzl7jdabbyg32x9bhirv3sc29hif6yif466mq8xyip0n82g"; depends=[colourpicker DAPAR DAPARdata data_table DT future highcharter htmlwidgets later promises R_utils rhandsontable sass shiny shinyAce shinyBS shinycssloaders shinyjqui shinyjs shinythemes shinyWidgets tibble webshot XML]; };
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ProtGenerics = derive2 { name="ProtGenerics"; version="1.28.0"; sha256="04hcgj4q8dbzp1a29rbww2bxxrg679pgys3m09p0ydkpsx76rq05"; depends=[]; };
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ProteoDisco = derive2 { name="ProteoDisco"; version="1.2.0"; sha256="1929aarf9al6di1r6z2n2ggdzblmfidikwswfg53nqanwwms31wa"; depends=[BiocGenerics BiocParallel Biostrings checkmate cleaver dplyr GenomeInfoDb GenomicFeatures GenomicRanges IRanges ParallelLogger plyr rlang S4Vectors tibble tidyr VariantAnnotation XVector]; };
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ProteoMM = derive2 { name="ProteoMM"; version="1.14.0"; sha256="0l5h4s77bv5wj6kj0zyj517acydqvd2sbxgl2fd22c1igwj9iqyl"; depends=[biomaRt gdata ggplot2 ggrepel gtools matrixStats]; };
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@ -777,7 +777,7 @@ in with self; {
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RDRToolbox = derive2 { name="RDRToolbox"; version="1.46.0"; sha256="13c7701g9n6irqpfc1bcamg2pys8vsryq1y6q9mw28im73wf0caw"; depends=[MASS rgl]; };
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REBET = derive2 { name="REBET"; version="1.14.0"; sha256="03v6qdc9hz2p74s64v0vk4wxc4nkl4g465ygdnnyxk2qz99q79qa"; depends=[ASSET]; };
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REDseq = derive2 { name="REDseq"; version="1.42.0"; sha256="16iqqzk7jlwb3yzsamxmpm0424a7hphv5ajbfw9fzmsshll3q18p"; depends=[AnnotationDbi BiocGenerics Biostrings BSgenome BSgenome_Celegans_UCSC_ce2 ChIPpeakAnno IRanges multtest]; };
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REMP = derive2 { name="REMP"; version="1.19.1"; sha256="0j95z8kbyvgdcdscvnmwkxgs16pfdh6f5h655gryfmylil1nw03g"; depends=[AnnotationHub BiocGenerics BiocParallel Biostrings BSgenome caret doParallel foreach GenomeInfoDb GenomicRanges impute IRanges iterators kernlab minfi org_Hs_eg_db ranger readr rtracklayer S4Vectors settings SummarizedExperiment]; };
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REMP = derive2 { name="REMP"; version="1.20.1"; sha256="0176p0bjlmyp95ssiqkziyasm247n2jgv2ijcl34zy1d5jndv4gj"; depends=[AnnotationHub BiocGenerics BiocParallel Biostrings BSgenome caret doParallel foreach GenomeInfoDb GenomicRanges impute IRanges iterators kernlab minfi org_Hs_eg_db ranger readr rtracklayer S4Vectors settings SummarizedExperiment]; };
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RGMQL = derive2 { name="RGMQL"; version="1.16.0"; sha256="1bwcqh6hmxjwzszd2747yc9wadh1jj0dm04d9752vyf1hz5nnhkv"; depends=[BiocGenerics data_table dplyr GenomicRanges glue httr plyr RGMQLlib rJava rtracklayer S4Vectors xml2]; };
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RGSEA = derive2 { name="RGSEA"; version="1.30.0"; sha256="0p03fxf725c9ayk29ah48jd96ry3i0360mxphzmsdycc3sna6mrq"; depends=[BiocGenerics]; };
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RGraph2js = derive2 { name="RGraph2js"; version="1.24.0"; sha256="14ffqx419vd5qz1fbbdszvzvx4m8mqmd7sh4d0dyxy37k19l60q3"; depends=[digest graph rjson whisker]; };
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@ -789,7 +789,7 @@ in with self; {
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RLMM = derive2 { name="RLMM"; version="1.58.0"; sha256="0rmir7ab8bs45c1q49yf6apx9i4sr673b33zw12hmp76zlgabwsi"; depends=[MASS]; };
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RLSeq = derive2 { name="RLSeq"; version="1.2.0"; sha256="0lka8q9hpv3kx8xlx6glsdhc1z7y0ihfdi2qglsggy4iyzdnav0d"; depends=[AnnotationHub aws_s3 callr caretEnsemble circlize ComplexHeatmap dplyr GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 ggplotify ggprism pheatmap RColorBrewer regioneR RLHub rtracklayer valr VennDiagram]; };
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RLassoCox = derive2 { name="RLassoCox"; version="1.4.0"; sha256="19kvnhxwvw652cng9ngq2d9dnfaqxxd9qjsvhaqv8kb4kz2r9bfb"; depends=[glmnet igraph Matrix survival]; };
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RMassBank = derive2 { name="RMassBank"; version="3.5.4"; sha256="05lkk38h8p7hx2ymm2ry946wmqkvkkfc7qp0fa8wjsqibq13qim6"; depends=[assertthat Biobase ChemmineOB ChemmineR data_table digest enviPat httr logger MSnbase mzR R_utils rcdk Rcpp RCurl readJDX rjson S4Vectors webchem XML yaml]; };
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RMassBank = derive2 { name="RMassBank"; version="3.6.1"; sha256="013j46ypgvr99j2grcxp251q8178a0x0xcsn9spdwba0cis2p836"; depends=[assertthat Biobase ChemmineOB ChemmineR data_table digest enviPat httr logger MSnbase mzR R_utils rcdk Rcpp RCurl readJDX rjson S4Vectors webchem XML yaml]; };
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RNAAgeCalc = derive2 { name="RNAAgeCalc"; version="1.8.0"; sha256="10d320bcdmn6mzcvivbphygnirs1znf1rnmirhzl1f978m50jp9j"; depends=[AnnotationDbi ggplot2 impute org_Hs_eg_db recount SummarizedExperiment]; };
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RNASeqPower = derive2 { name="RNASeqPower"; version="1.36.0"; sha256="0bv9xkkg30vr9lmybiialh0mimcvmcrsf0wm23r6jsmm8pqgv7wd"; depends=[]; };
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RNAdecay = derive2 { name="RNAdecay"; version="1.16.0"; sha256="0skv7hx83yq9c426am81555imdbbkysckv8py5ng3q56r67cgy45"; depends=[ggplot2 gplots nloptr scales TMB]; };
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@ -832,7 +832,7 @@ in with self; {
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Rbwa = derive2 { name="Rbwa"; version="1.0.0"; sha256="1rf43p87p5397cbh9znl0qvrplid102qd3bgf310kk3kpkjdw56q"; depends=[]; };
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Rcade = derive2 { name="Rcade"; version="1.37.0"; sha256="1x8a4kas3bd4dzlwwiw781l9j2xa4sqmwbzblmsc23cp7kfbvffg"; depends=[baySeq GenomeInfoDb GenomicAlignments GenomicRanges IRanges plotrix rgl Rsamtools S4Vectors]; };
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RcisTarget = derive2 { name="RcisTarget"; version="1.16.0"; sha256="17fnjkg6rjqj33v7slg81skqag10y6dc14g5iv69gqshjal4w4im"; depends=[arrow AUCell BiocGenerics data_table dplyr GenomeInfoDb GenomicRanges GSEABase R_utils S4Vectors SummarizedExperiment tibble]; };
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Rcpi = derive2 { name="Rcpi"; version="1.32.0"; sha256="15igxc8ki7gy3ca01r85zqi1j4j31hdhwhcmdbnkv9z6f3r8i38m"; depends=[Biostrings doParallel foreach GOSemSim rcdk RCurl rjson]; };
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Rcpi = derive2 { name="Rcpi"; version="1.32.1"; sha256="0py2m77qkxw68qiir8rnls8j1l5rdn0l30483rv3n4fqxldhavb8"; depends=[Biostrings doParallel foreach GOSemSim rcdk RCurl rjson]; };
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Rcwl = derive2 { name="Rcwl"; version="1.12.0"; sha256="1q10gzh3m46jaac1w5hhfv166vrh23q3fwn377cy0p0cq6mhqk9j"; depends=[basilisk batchtools BiocParallel codetools DiagrammeR R_utils S4Vectors shiny yaml]; };
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RcwlPipelines = derive2 { name="RcwlPipelines"; version="1.12.0"; sha256="1lcx926y437jkphldnydw71k64mibgh5k0cwxzsf8f9b0lwmhl02"; depends=[BiocFileCache git2r httr rappdirs Rcwl S4Vectors]; };
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Rdisop = derive2 { name="Rdisop"; version="1.56.0"; sha256="0cy1m1mch6d7csvlaacb5c54nz3f4caddjyfwbxq74qbzgx8mq07"; depends=[Rcpp]; };
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@ -852,7 +852,7 @@ in with self; {
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Rfastp = derive2 { name="Rfastp"; version="1.6.0"; sha256="06zzmdym2x72a99853qvh1a4snbmgysnmi6yckakdg6isizxm14p"; depends=[ggplot2 Rcpp reshape2 Rhtslib rjson zlibbioc]; };
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Rgin = derive2 { name="Rgin"; version="1.15.0"; sha256="1x5zj2d5rvsr2xh0ifpnrys9v91dal1xxhv5mmk16rs8wzwqpqba"; depends=[RcppEigen]; };
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Rgraphviz = derive2 { name="Rgraphviz"; version="2.40.0"; sha256="1r6ff7w2bmyfl1vzjvpgnhb8f5arwjlpab8fw5ph8fgyiqbcx94l"; depends=[graph]; };
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Rhdf5lib = derive2 { name="Rhdf5lib"; version="1.18.0"; sha256="0q49plxjw1akrglvh2iqiq4gx30ph1sfa5zqy2s7vxm2d73cylyj"; depends=[]; };
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Rhdf5lib = derive2 { name="Rhdf5lib"; version="1.18.2"; sha256="1jpb8h7c724yz51zjfqs90bsqxgmy1rry2ra9qamsgqpr2j9764g"; depends=[]; };
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Rhisat2 = derive2 { name="Rhisat2"; version="1.12.0"; sha256="0hzair41l47kzykymd169a34pfhb98vrjgkgdf15m17csyz7pnv7"; depends=[GenomicFeatures GenomicRanges SGSeq]; };
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Rhtslib = derive2 { name="Rhtslib"; version="1.28.0"; sha256="07kws6afkxbmxq4w357mwwl712pdd16alvz7iqijjd2x7rjchj2f"; depends=[zlibbioc]; };
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RiboCrypt = derive2 { name="RiboCrypt"; version="1.2.0"; sha256="071y96ilsb9l5jfdsyhjpm69aqz8v8hjis2izvqwvds4ia2j1mhh"; depends=[BiocGenerics BiocParallel Biostrings data_table dplyr GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 IRanges ORFik plotly rlang]; };
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@ -869,7 +869,7 @@ in with self; {
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RpsiXML = derive2 { name="RpsiXML"; version="2.38.0"; sha256="0x4nph4xss4piq4fgijjjj33yrqqfdbsgn9wvqy17nglvz5gi7bi"; depends=[annotate AnnotationDbi Biobase graph hypergraph RBGL XML]; };
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Rqc = derive2 { name="Rqc"; version="1.30.0"; sha256="11j8m69zdcmpjb3xzr4s8sqmv8aqgl8q7k81gnd09l3nyjzy0h1k"; depends=[BiocGenerics BiocParallel BiocStyle Biostrings biovizBase GenomicAlignments GenomicFiles ggplot2 IRanges knitr markdown plyr Rcpp reshape2 Rsamtools S4Vectors shiny ShortRead]; };
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Rsamtools = derive2 { name="Rsamtools"; version="2.12.0"; sha256="1wll703if12qrn0d11ljwf7rqhs4lb27fzyyz1hqwvzn3v361s10"; depends=[BiocGenerics BiocParallel Biostrings bitops GenomeInfoDb GenomicRanges IRanges Rhtslib S4Vectors XVector zlibbioc]; };
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Rsubread = derive2 { name="Rsubread"; version="2.10.0"; sha256="1fd83w8yzajd7ybkjyk68njkg39sq9a4bcgdnfj0lg6n33gbnv7w"; depends=[Matrix]; };
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Rsubread = derive2 { name="Rsubread"; version="2.10.3"; sha256="0s89h600dgrzkjfrrk283i1y8kwr233rk5x91dgss60x38fzjv02"; depends=[Matrix]; };
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Rtpca = derive2 { name="Rtpca"; version="1.6.0"; sha256="1cv0yj3j2cndyb0827raw3x7gi3li0nj2q0s71apj2bvl74y2h27"; depends=[Biobase dplyr fdrtool ggplot2 pROC tibble tidyr]; };
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Rtreemix = derive2 { name="Rtreemix"; version="1.58.0"; sha256="0n9pmmn0mzj6zi303zzkmcww8f23xydgvw6bz5cx7sswlqvsixvm"; depends=[Biobase graph Hmisc]; };
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S4Vectors = derive2 { name="S4Vectors"; version="0.34.0"; sha256="0j3ybhzdhlhw8527nks3mjja28asjya2n0m0rjkh4bw66rkfys4k"; depends=[BiocGenerics]; };
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@ -903,7 +903,7 @@ in with self; {
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SMAP = derive2 { name="SMAP"; version="1.60.0"; sha256="11c0br8kv93bzdn4y4xrkl6pkqdpn4zzyx31dqkq5bz4vvjfmz47"; depends=[]; };
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SMITE = derive2 { name="SMITE"; version="1.24.0"; sha256="0klqxzaypidfzgcxfa1lnrlsv08zkqwf5y82ldac7bpnnyr91z1b"; depends=[AnnotationDbi Biobase BioNet geneLenDataBase GenomicRanges ggplot2 goseq Hmisc igraph IRanges KEGGREST org_Hs_eg_db plyr reactome_db S4Vectors scales]; };
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SNAGEE = derive2 { name="SNAGEE"; version="1.36.0"; sha256="0zjn0qjyhpnfzabgi5rv1zhblfwz4rdldp7pa18zkayflhfhql5i"; depends=[SNAGEEdata]; };
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SNPRelate = derive2 { name="SNPRelate"; version="1.30.0"; sha256="1jbmicz4xnf6v3cb328x0z1rwd3zcm2l72lgih0hx306wd3g0i29"; depends=[gdsfmt]; };
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SNPRelate = derive2 { name="SNPRelate"; version="1.30.1"; sha256="1j3cz45g0bm48hqm6zm8zyfsmjb08cb7p52yw8r4jmld3jci33cr"; depends=[gdsfmt]; };
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SNPediaR = derive2 { name="SNPediaR"; version="1.22.0"; sha256="1qg1arrf9pv59hzmncmfhw9w2npk6mm068c6ghx527vja7g3lcxd"; depends=[jsonlite RCurl]; };
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SNPhood = derive2 { name="SNPhood"; version="1.26.0"; sha256="186qcscxgpjxc3c875yvnc75xv4dmmjpy7ci2glabw9sy5p2vz2a"; depends=[BiocGenerics BiocParallel Biostrings checkmate cluster data_table DESeq2 GenomeInfoDb GenomicRanges ggplot2 gridExtra IRanges lattice RColorBrewer reshape2 Rsamtools S4Vectors scales SummarizedExperiment VariantAnnotation]; };
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SOMNiBUS = derive2 { name="SOMNiBUS"; version="1.4.0"; sha256="0xjrn2anfsw6d48lb2kp1zxj2d4cn6gr6wb6cfllwxiwdq635lyc"; depends=[Matrix mgcv VGAM]; };
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@ -918,7 +918,7 @@ in with self; {
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SRAdb = derive2 { name="SRAdb"; version="1.58.0"; sha256="1r21llikjjicbqsrcp3yaqsp45nbzbrccsn4gpgdk90gx7p325by"; depends=[GEOquery graph RCurl RSQLite]; };
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STAN = derive2 { name="STAN"; version="2.24.0"; sha256="18qa8fa6n9n965h0rwbsyfd14snh2n96rwfi1l1dg7wdrksyr8wx"; depends=[BiocGenerics GenomeInfoDb GenomicRanges Gviz IRanges poilog Rsolnp S4Vectors]; };
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STATegRa = derive2 { name="STATegRa"; version="1.32.0"; sha256="157jm77mh12p5wdik1xm00p8r7x692gw5sb2dphkjf6fkc53sxk0"; depends=[affy Biobase calibrate edgeR foreach ggplot2 gplots gridExtra limma MASS]; };
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STRINGdb = derive2 { name="STRINGdb"; version="2.8.0"; sha256="194grs69q20irpqmck7fb9alp9764hy3is132yzpfsicj72vpbyw"; depends=[gplots hash igraph plotrix plyr png RColorBrewer RCurl sqldf]; };
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STRINGdb = derive2 { name="STRINGdb"; version="2.8.4"; sha256="1jn6080v6097zpqsr4gfbx31gqqdhpzjrk63avk3v3xwawmf2379"; depends=[gplots hash igraph plotrix plyr png RColorBrewer RCurl sqldf]; };
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STROMA4 = derive2 { name="STROMA4"; version="1.20.0"; sha256="14qz7napk9kmga7gvhp34zh0kdkwzqx57q79famz1lyanzvibcij"; depends=[Biobase BiocParallel cluster matrixStats]; };
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STdeconvolve = derive2 { name="STdeconvolve"; version="1.0.0"; sha256="092gsmnp70wqpw21yxicpm29qwp27zxz60d026i6mfszhd48abxx"; depends=[BiocParallel clue ggplot2 liger Matrix mgcv reshape2 scatterpie slam topicmodels viridis]; };
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SWATH2stats = derive2 { name="SWATH2stats"; version="1.26.0"; sha256="0n6ap58lbn3rbaqb50244byam2fc62q85zl2a5bws5bsfccnvzk3"; depends=[biomaRt data_table ggplot2 reshape2]; };
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@ -952,7 +952,7 @@ in with self; {
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SpatialExperiment = derive2 { name="SpatialExperiment"; version="1.6.0"; sha256="0r4xvmd6kf2ksc1ma68118nfw8adi2ncf69r6dp5fw2hgfph9c6p"; depends=[BiocFileCache BiocGenerics DropletUtils magick rjson S4Vectors SingleCellExperiment SummarizedExperiment]; };
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SpeCond = derive2 { name="SpeCond"; version="1.50.0"; sha256="051p6npzjpwagd0bnzpbdjcmgkasr8d74a42ppmlc9hsfg8pzqcw"; depends=[Biobase fields hwriter mclust RColorBrewer]; };
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Spectra = derive2 { name="Spectra"; version="1.6.0"; sha256="0kzz7par5zwk4qypicmz39d6bc4aqmflzzxfrpng2y3id7f15jks"; depends=[BiocGenerics BiocParallel fs IRanges MsCoreUtils ProtGenerics S4Vectors]; };
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SpectralTAD = derive2 { name="SpectralTAD"; version="1.12.0"; sha256="0svv4mp6qk2k3clz8qdigzhawh4cglzwrb8frh5c6mgrgdbf53g5"; depends=[BiocParallel cluster dplyr GenomicRanges HiCcompare magrittr Matrix PRIMME]; };
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SpectralTAD = derive2 { name="SpectralTAD"; version="1.12.0"; sha256="0svv4mp6qk2k3clz8qdigzhawh4cglzwrb8frh5c6mgrgdbf53g5"; depends=[BiocParallel cluster dplyr GenomicRanges HiCcompare magrittr Matrix]; };
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SpidermiR = derive2 { name="SpidermiR"; version="1.26.0"; sha256="0v1sdcwrhvnkr497i6qifzvzg2sr3ml5w2pwrp6nhlfhp1g0l4ah"; depends=[AnnotationDbi gdata ggplot2 gplots gridExtra httr igraph lattice latticeExtra MAGeCKFlute miRNAtap miRNAtap_db org_Hs_eg_db TCGAbiolinks]; };
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SplicingFactory = derive2 { name="SplicingFactory"; version="1.4.0"; sha256="11kkr4c2ilwbr2h80aqiphxihwzs4sr23hq3q6w22w3wqqp7w24k"; depends=[SummarizedExperiment]; };
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SplicingGraphs = derive2 { name="SplicingGraphs"; version="1.36.0"; sha256="1c8m8ab5jrwa8fryrdww4r41svkv864l2pr1hy1kil3njyaam0ml"; depends=[BiocGenerics BiocParallel GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges graph igraph IRanges Rgraphviz Rsamtools S4Vectors]; };
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@ -967,17 +967,17 @@ in with self; {
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Sushi = derive2 { name="Sushi"; version="1.34.0"; sha256="0adswrbzd93rhy3q56ypwkrk6155vd4zxapvznswyjlxp8ha813q"; depends=[biomaRt zoo]; };
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SwathXtend = derive2 { name="SwathXtend"; version="2.18.0"; sha256="02lkh200pvzps2vp0i4fjm96zi1fy8x21kvd0sa599yks7vimzp4"; depends=[e1071 lattice openxlsx VennDiagram]; };
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SynExtend = derive2 { name="SynExtend"; version="1.8.0"; sha256="0z30izc2wnbbhv19xf5dnnls8j42v38771yv78im75li88zxl91m"; depends=[Biostrings DECIPHER IRanges S4Vectors]; };
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SynMut = derive2 { name="SynMut"; version="1.12.0"; sha256="1bm9z9za584x56qvpgqb5frhj02kfdy336q8ridlk1b83j2fmx23"; depends=[BiocGenerics Biostrings seqinr stringr]; };
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TADCompare = derive2 { name="TADCompare"; version="1.6.0"; sha256="0ramji5pn5w7ch83slflsw1wxhy451zw99rkhzb4slvgqi8v7bk8"; depends=[cluster cowplot dplyr ggplot2 ggpubr HiCcompare magrittr Matrix PRIMME RColorBrewer reshape2 tidyr]; };
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SynMut = derive2 { name="SynMut"; version="1.12.1"; sha256="0smrqh2gk1cy8aqqrfx7whwdcsn5s57w6crkah2v50p1q9xbvgjm"; depends=[BiocGenerics Biostrings seqinr stringr]; };
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TADCompare = derive2 { name="TADCompare"; version="1.6.0"; sha256="0ramji5pn5w7ch83slflsw1wxhy451zw99rkhzb4slvgqi8v7bk8"; depends=[cluster cowplot dplyr ggplot2 ggpubr HiCcompare magrittr Matrix RColorBrewer reshape2 tidyr]; };
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TAPseq = derive2 { name="TAPseq"; version="1.8.0"; sha256="0ls9l12fp04j2asr25cbz6xs38y3znhgcphfglbc13li3aa77gx0"; depends=[BiocGenerics BiocParallel Biostrings BSgenome dplyr GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges S4Vectors tidyr]; };
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TBSignatureProfiler = derive2 { name="TBSignatureProfiler"; version="1.8.0"; sha256="1npcdr3grm6qq4lqan6z9czkiwyz74pi741jwahzr0q93ah25kks"; depends=[ASSIGN BiocGenerics BiocParallel ComplexHeatmap DESeq2 DT edgeR gdata ggplot2 GSVA magrittr RColorBrewer reshape2 rlang ROCit S4Vectors singscore SummarizedExperiment]; };
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TCC = derive2 { name="TCC"; version="1.36.0"; sha256="077gj5f1iwb3xwy29p5q5fr3459nq9swybn7504dyxb93259qxzi"; depends=[baySeq DESeq2 edgeR ROC]; };
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TCGAbiolinks = derive2 { name="TCGAbiolinks"; version="2.24.0"; sha256="19wf7bzspwanj0wfsqqmzh29iz6rc41rdr2xbzw8jlm2wspsqjbs"; depends=[biomaRt data_table downloader dplyr GenomicRanges ggplot2 httr IRanges jsonlite knitr plyr purrr R_utils readr rvest S4Vectors stringr SummarizedExperiment TCGAbiolinksGUI_data tibble tidyr XML xml2]; };
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TCGAbiolinks = derive2 { name="TCGAbiolinks"; version="2.24.3"; sha256="0visvfhzaf0p1rb5vjkmw1c91zfxpks8nl9nbl9xlnpm8lkmmkms"; depends=[biomaRt data_table downloader dplyr GenomicRanges ggplot2 httr IRanges jsonlite knitr plyr purrr R_utils readr rvest S4Vectors stringr SummarizedExperiment TCGAbiolinksGUI_data tibble tidyr XML xml2]; };
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TCGAbiolinksGUI = derive2 { name="TCGAbiolinksGUI"; version="1.22.0"; sha256="1rav6nmbq8sn60x6cdc5zmvwwpiyfjc6n8hlzyjsg2yy3h3ij0qp"; depends=[caret clusterProfiler colourpicker data_table downloader DT ELMER ggplot2 ggrepel maftools pathview plotly readr sesame shiny shinyBS shinydashboard shinyFiles shinyjs stringr SummarizedExperiment TCGAbiolinks TCGAbiolinksGUI_data]; };
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TCGAutils = derive2 { name="TCGAutils"; version="1.16.0"; sha256="0xh2z8055az6hnr2a3rsjlz9x7i4vz82dywk67xzmjf7954b1qhc"; depends=[AnnotationDbi BiocGenerics GenomeInfoDb GenomicDataCommons GenomicFeatures GenomicRanges IRanges MultiAssayExperiment RaggedExperiment rvest S4Vectors stringr SummarizedExperiment xml2]; };
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TCseq = derive2 { name="TCseq"; version="1.20.0"; sha256="0wqkbvg41xbkfc0xs44ckpzagwyfmqrdr69fj7am51khzv7gznrk"; depends=[BiocGenerics cluster e1071 edgeR GenomicAlignments GenomicRanges ggplot2 IRanges locfit reshape2 Rsamtools SummarizedExperiment]; };
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TDARACNE = derive2 { name="TDARACNE"; version="1.46.0"; sha256="1ryrnaaq15sgji2j4js5vgsr2j7dl4dd0shmz7qayyq0k7ai2yaq"; depends=[Biobase GenKern Rgraphviz]; };
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TEKRABber = derive2 { name="TEKRABber"; version="0.99.91"; sha256="0cmwcmk10piwh762w79z10grnnk4l87lnchqiwcxzscmrphcwijj"; depends=[apeglm biomaRt DESeq2 Rcpp SCBN SummarizedExperiment]; };
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TDARACNE = derive2 { name="TDARACNE"; version="1.46.0"; sha256="1ryrnaaq15sgji2j4js5vgsr2j7dl4dd0shmz7qayyq0k7ai2yaq"; depends=[Biobase Rgraphviz]; };
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TEKRABber = derive2 { name="TEKRABber"; version="1.0.1"; sha256="0pilrjrvd43jr8h6s2zcc6rk0p4q2l3bhz6lm344a7y5wyvccly6"; depends=[apeglm biomaRt DESeq2 Rcpp SCBN SummarizedExperiment]; };
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TEQC = derive2 { name="TEQC"; version="4.18.0"; sha256="1n0ifh86z4635x8hk4yv8n1ay35725i7y0n8j2gdp7si5y3nsfnv"; depends=[Biobase BiocGenerics hwriter IRanges Rsamtools]; };
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TFARM = derive2 { name="TFARM"; version="1.18.0"; sha256="0rmw7r6k8mb5672aap26liqblrmasxvccxd4fjw2sdb449wbd9dl"; depends=[arules fields GenomicRanges gplots stringr]; };
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TFBSTools = derive2 { name="TFBSTools"; version="1.34.0"; sha256="0l6j1r2cx7jfd39qzbyynk4jvzd81ys6yypzxjc97js4kkyrx29w"; depends=[Biobase BiocGenerics BiocParallel Biostrings BSgenome caTools CNEr DBI DirichletMultinomial GenomeInfoDb GenomicRanges gtools IRanges RSQLite rtracklayer S4Vectors seqLogo TFMPvalue XML XVector]; };
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@ -990,7 +990,7 @@ in with self; {
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TOAST = derive2 { name="TOAST"; version="1.10.0"; sha256="1m9zg2k0z22369ly48swccmgqwfw20rv2bm18d23zdafmkb7jklj"; depends=[corpcor doParallel EpiDISH GGally ggplot2 limma nnls quadprog SummarizedExperiment tidyr]; };
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TPP = derive2 { name="TPP"; version="3.24.0"; sha256="0w0gwhvc2mra0jd81pskhqsdayikz3fpbcx0sf45iac918dd2m4l"; depends=[Biobase biobroom broom data_table doParallel dplyr foreach futile_logger ggplot2 gridExtra knitr limma magrittr MASS mefa nls2 openxlsx plyr purrr RColorBrewer RCurl reshape2 rmarkdown stringr tibble tidyr VennDiagram VGAM]; };
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TPP2D = derive2 { name="TPP2D"; version="1.12.0"; sha256="1567r1v92skhlvjysh5v32h6c50grm8qm7wbwdvr52pjqc7kvfb4"; depends=[BiocParallel doParallel dplyr foreach ggplot2 limma MASS openxlsx RCurl stringr tidyr]; };
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TREG = derive2 { name="TREG"; version="1.0.0"; sha256="0hxk7b94cz2dmbkqf3798a4ycvbxs2cgl99vwcc75nw40fygwbf8"; depends=[Matrix purrr rafalib SummarizedExperiment]; };
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TREG = derive2 { name="TREG"; version="1.0.1"; sha256="1d0ynkj1iiirigrzbnfclzcvvz1yx8c0ykqhz5vg8bhaw1h0ry3j"; depends=[Matrix purrr rafalib SummarizedExperiment]; };
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TRESS = derive2 { name="TRESS"; version="1.2.0"; sha256="17g37g8kbis42iv980002py225cxy0gvjfnjda760am387gb9hqm"; depends=[AnnotationDbi GenomicFeatures GenomicRanges IRanges Matrix matrixStats Rsamtools rtracklayer S4Vectors]; };
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TRONCO = derive2 { name="TRONCO"; version="2.28.0"; sha256="1ynf41bpc0v51sv6mig84n778kpfq0l9g50xff1bwz7zl1iab4al"; depends=[bnlearn circlize doParallel foreach gridExtra gtable gtools igraph iterators R_matlab RColorBrewer Rgraphviz scales xtable]; };
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TSCAN = derive2 { name="TSCAN"; version="1.34.0"; sha256="0a8f38jbb2lhqavqgbvm0d9xfy1cgjq4l7vs5h6kr45ij09wr6pm"; depends=[combinat DelayedArray fastICA ggplot2 gplots igraph Matrix mclust mgcv plyr S4Vectors shiny SingleCellExperiment SummarizedExperiment TrajectoryUtils]; };
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@ -1007,7 +1007,7 @@ in with self; {
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TitanCNA = derive2 { name="TitanCNA"; version="1.34.0"; sha256="14mxskynm6rjh8c7nzkp06c7a3a5rlcj88s9c6brzgx7gm3k7j3x"; depends=[BiocGenerics data_table dplyr foreach GenomeInfoDb GenomicRanges IRanges VariantAnnotation]; };
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TnT = derive2 { name="TnT"; version="1.18.0"; sha256="01c4lhy9k2wiy7m7685qy4bj5q9bys7xqxfy9x3kpcn7by3dix83"; depends=[Biobase data_table GenomeInfoDb GenomicRanges htmlwidgets IRanges jsonlite knitr S4Vectors]; };
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ToxicoGx = derive2 { name="ToxicoGx"; version="2.0.0"; sha256="0d331md9cq2h44zq8wvj2167994i097drfgljhwj1nnfsx9agqn1"; depends=[assertthat Biobase BiocGenerics BiocParallel caTools CoreGx data_table downloader dplyr ggplot2 jsonlite limma magrittr reshape2 S4Vectors scales SummarizedExperiment tibble tidyr]; };
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TraRe = derive2 { name="TraRe"; version="1.4.0"; sha256="1vrafzf8qk6nnav1m4ym26n8f0nfbsxqnmymv9a7k8yfxry3jnn8"; depends=[BiocParallel dqrng ggplot2 glmnet gplots gtools hash igraph matrixStats pvclust R_utils SummarizedExperiment vbsr]; };
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TraRe = derive2 { name="TraRe"; version="1.4.0"; sha256="1vrafzf8qk6nnav1m4ym26n8f0nfbsxqnmymv9a7k8yfxry3jnn8"; depends=[BiocParallel dqrng ggplot2 glmnet gplots gtools hash igraph matrixStats pvclust R_utils SummarizedExperiment]; };
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TrajectoryGeometry = derive2 { name="TrajectoryGeometry"; version="1.4.0"; sha256="13dxsk2dq5bsf9bwq4618kr6wsbmvzqnqh8i8zqrx4i818wd571s"; depends=[ggplot2 pracma rgl]; };
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TrajectoryUtils = derive2 { name="TrajectoryUtils"; version="1.4.0"; sha256="07hcr3zplxlzlwc13wh9006m5kaqm57cm1b2x74bpp857f2q93dj"; depends=[igraph Matrix S4Vectors SingleCellExperiment SummarizedExperiment]; };
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TransView = derive2 { name="TransView"; version="1.40.0"; sha256="1k3fs0wxh2m2mp7i6hqnpgf60jikgjn7cdv2mmnz77ignp37xr4f"; depends=[BiocGenerics GenomicRanges gplots IRanges Rhtslib S4Vectors zlibbioc]; };
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@ -1017,19 +1017,19 @@ in with self; {
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Trendy = derive2 { name="Trendy"; version="1.18.0"; sha256="06rjim93kqrf7l2m16vgi567fi9cdblgbf9khnmmbg73kaa346zz"; depends=[BiocParallel DT gplots magrittr S4Vectors segmented shiny shinyFiles SummarizedExperiment]; };
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TurboNorm = derive2 { name="TurboNorm"; version="1.44.0"; sha256="00rggbdsk7xprkry8bi17mf143kqgw63cb315d9dc1qrc9vyz568"; depends=[affy convert lattice limma marray]; };
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TypeInfo = derive2 { name="TypeInfo"; version="1.62.0"; sha256="17cj4yd6lpckidzh5f3jb3vbwyimlnmsb3v5as4f91h2vnymwpax"; depends=[]; };
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UCell = derive2 { name="UCell"; version="2.0.0"; sha256="0p7jv1rl9vs1ag8a4vnkdghzixa3dljixkrhacfi69qm6crjlg12"; depends=[BiocParallel data_table Matrix SingleCellExperiment SummarizedExperiment]; };
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UCell = derive2 { name="UCell"; version="2.0.1"; sha256="08wh5fch4sb1ijjz8rr8jkz3vvskb7k7948fd2b7bb104qmyhv41"; depends=[BiocParallel data_table Matrix SingleCellExperiment SummarizedExperiment]; };
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UMI4Cats = derive2 { name="UMI4Cats"; version="1.6.0"; sha256="0216qwriwjm0m7rzq8qjrvhnmn0fyqsv13cx24is53wqkqbqnavm"; depends=[annotate BiocFileCache BiocGenerics Biostrings BSgenome cowplot DESeq2 dplyr fda GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 IRanges magick magrittr org_Hs_eg_db R_utils rappdirs Rbowtie2 RColorBrewer regioneR reshape2 rlang Rsamtools S4Vectors scales ShortRead stringr SummarizedExperiment TxDb_Hsapiens_UCSC_hg19_knownGene zoo]; };
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UNDO = derive2 { name="UNDO"; version="1.38.0"; sha256="0fasad2y0cnrdlfarqxlmgn30hjfqksddnvq5yia3ps50wzj7xyr"; depends=[Biobase BiocGenerics boot MASS nnls]; };
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Ularcirc = derive2 { name="Ularcirc"; version="1.14.0"; sha256="0pqinw35vd94gk78i45rdyl4gyp6q8dmzc5kz72mcfg702wh7g8h"; depends=[AnnotationDbi AnnotationHub BiocGenerics Biostrings BSgenome data_table DT GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges ggplot2 ggrepel gsubfn mirbase_db moments Organism_dplyr plotgardener R_utils S4Vectors shiny shinydashboard shinyFiles shinyjs yaml]; };
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UniProt_ws = derive2 { name="UniProt.ws"; version="2.36.0"; sha256="0s63wpgcmg98ykccb8bcwnjzawz9isc4mxz4cirhb9dxl95axq3h"; depends=[AnnotationDbi BiocFileCache BiocGenerics httr rappdirs RSQLite]; };
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Uniquorn = derive2 { name="Uniquorn"; version="2.16.0"; sha256="0hf2gs0aw0jw9qw1bqhsvxvw5grppbi3wxbfiynkbvza11aglifw"; depends=[doParallel foreach GenomicRanges IRanges R_utils stringr VariantAnnotation WriteXLS]; };
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VAExprs = derive2 { name="VAExprs"; version="1.1.1"; sha256="026gipywc4xmap4p4x9wdmfd4208rx57bv5l8b2l1sd16wxvcazk"; depends=[CatEncoders DeepPINCS DiagrammeR keras mclust purrr scater SingleCellExperiment SummarizedExperiment tensorflow]; };
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VAExprs = derive2 { name="VAExprs"; version="1.2.1"; sha256="19jhjayyaga1lyswhbibgva32mdmfvkdidcvxgl22728c6ppkg61"; depends=[CatEncoders DeepPINCS DiagrammeR keras mclust purrr scater SingleCellExperiment SummarizedExperiment tensorflow]; };
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VCFArray = derive2 { name="VCFArray"; version="1.12.0"; sha256="17zgwv8nc192jyzlym09zyqppbg6zlid60xzh921mvp41sprf2j9"; depends=[BiocGenerics DelayedArray GenomicFiles GenomicRanges Rsamtools S4Vectors VariantAnnotation]; };
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VERSO = derive2 { name="VERSO"; version="1.6.0"; sha256="13s91s03l15sha9sqcwazhhzph7s7ivbijlq1cz6c04x54bsdncn"; depends=[ape Rfast]; };
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VaSP = derive2 { name="VaSP"; version="1.8.0"; sha256="10fvdlxj4flv4zssaprhzg76l0jlin015pha7dmvfmjda4xm2zrl"; depends=[ballgown cluster GenomeInfoDb GenomicAlignments GenomicRanges IRanges matrixStats Rsamtools S4Vectors]; };
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VanillaICE = derive2 { name="VanillaICE"; version="1.58.0"; sha256="1m3fi8snnf5rklhnwj2wndk86ry27anpa9pkk43v35qx5cvm1q9p"; depends=[Biobase BiocGenerics BSgenome_Hsapiens_UCSC_hg18 crlmm data_table foreach GenomeInfoDb GenomicRanges IRanges lattice MatrixGenerics matrixStats oligoClasses S4Vectors SummarizedExperiment]; };
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VarCon = derive2 { name="VarCon"; version="1.4.0"; sha256="0l0vgs2hmykkxp2s14pzwjzg3xbhcj5md3hfz85n0cn4j8qgf4hz"; depends=[Biostrings BSgenome GenomicRanges ggplot2 IRanges shiny shinycssloaders shinyFiles]; };
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VariantAnnotation = derive2 { name="VariantAnnotation"; version="1.42.0"; sha256="0vda6xlraflp1i759a21ygba28ivn5g44i8fbsylk7j1klbhbbiz"; depends=[AnnotationDbi Biobase BiocGenerics Biostrings BSgenome DBI GenomeInfoDb GenomicFeatures GenomicRanges IRanges MatrixGenerics Rhtslib Rsamtools rtracklayer S4Vectors SummarizedExperiment XVector zlibbioc]; };
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VariantAnnotation = derive2 { name="VariantAnnotation"; version="1.42.1"; sha256="12d5hkx6pby6l2asyg4jp4jb2x17ybwhqd55rl64h37mwcndbdg1"; depends=[AnnotationDbi Biobase BiocGenerics Biostrings BSgenome DBI GenomeInfoDb GenomicFeatures GenomicRanges IRanges MatrixGenerics Rhtslib Rsamtools rtracklayer S4Vectors SummarizedExperiment XVector zlibbioc]; };
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VariantExperiment = derive2 { name="VariantExperiment"; version="1.10.0"; sha256="17xrlmr25iilrnmsicf42qc7alh8qfqg6v7sd5mpw4lzwxim1mqv"; depends=[Biostrings DelayedArray DelayedDataFrame GDSArray gdsfmt GenomicRanges IRanges S4Vectors SeqArray SeqVarTools SNPRelate SummarizedExperiment]; };
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VariantFiltering = derive2 { name="VariantFiltering"; version="1.32.0"; sha256="1bjqn8qik221x0bqvgd99p87v45iihwp6cxckh4ks964pd0c1xk8"; depends=[AnnotationDbi Biobase BiocGenerics BiocParallel Biostrings BSgenome DT GenomeInfoDb GenomicFeatures GenomicRanges GenomicScores graph Gviz IRanges RBGL Rsamtools S4Vectors shiny shinyjs shinythemes shinyTree SummarizedExperiment VariantAnnotation XVector]; };
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VariantTools = derive2 { name="VariantTools"; version="1.38.0"; sha256="18nxcamfgnw4n2ab0czxglw0sqc9wzdqzpjv43lcyyal23lzzsix"; depends=[Biobase BiocGenerics BiocParallel Biostrings BSgenome GenomeInfoDb GenomicFeatures GenomicRanges IRanges Matrix Rsamtools rtracklayer S4Vectors VariantAnnotation]; };
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@ -1061,13 +1061,13 @@ in with self; {
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affyILM = derive2 { name="affyILM"; version="1.48.0"; sha256="1rk68bhz2pyca4saiwd0kcw7sh2gs6d4c482jj4kx9r216mpb4q6"; depends=[affxparser affy Biobase gcrma]; };
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affyPLM = derive2 { name="affyPLM"; version="1.72.0"; sha256="1m3n5mvpg9g46rrglhdh94pppf71xp344yrcnw1i60vwv41vhbck"; depends=[affy Biobase BiocGenerics gcrma preprocessCore zlibbioc]; };
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affycomp = derive2 { name="affycomp"; version="1.72.0"; sha256="0aq5p56sqpvba0yhgd75302s9bazchh1izgymng6cpb78y5wfpj0"; depends=[Biobase]; };
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affycoretools = derive2 { name="affycoretools"; version="1.68.0"; sha256="14rrgq67hj6qn85wgwfq1frzy7x1pk1s7xg38cb65f6m4y5xx4wx"; depends=[affy AnnotationDbi Biobase BiocGenerics DBI edgeR gcrma ggplot2 Glimma GOstats gplots hwriter lattice limma oligoClasses ReportingTools RSQLite S4Vectors xtable]; };
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affycoretools = derive2 { name="affycoretools"; version="1.68.1"; sha256="05x64hy5jpmg973biwq4q9gzy1n0iqc0pxrix1f6bri1w6vil3ww"; depends=[affy AnnotationDbi Biobase BiocGenerics DBI edgeR gcrma ggplot2 Glimma GOstats gplots hwriter lattice limma oligoClasses ReportingTools RSQLite S4Vectors xtable]; };
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affyio = derive2 { name="affyio"; version="1.66.0"; sha256="19cw82qvzkz6vh2gm302y7digsf6xif7c9l2q9s6lkx2yflqpgfp"; depends=[zlibbioc]; };
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affylmGUI = derive2 { name="affylmGUI"; version="1.70.0"; sha256="0ic8cmssjpjkblrblfdpqqcaxn1izxk1hmcfdk1sphm7wfiw8l2n"; depends=[affy affyio affyPLM AnnotationDbi BiocGenerics BiocManager gcrma limma R2HTML tkrplot xtable]; };
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aggregateBioVar = derive2 { name="aggregateBioVar"; version="1.6.0"; sha256="0ngg12bgr95m4wm12scmrb55dgy4909c6qrg169l6dkng99v4nx1"; depends=[Matrix rlang S4Vectors SingleCellExperiment SummarizedExperiment tibble]; };
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agilp = derive2 { name="agilp"; version="3.28.0"; sha256="1pm329y2nfcnx98ggxq0prdd5pxfcl5iylvsjjnhw5lyz1awg1yf"; depends=[]; };
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airpart = derive2 { name="airpart"; version="1.4.0"; sha256="0ljankgvgf8rby4z340wxx8v7acs9yz955p3a40jl6y8rz1svc06"; depends=[apeglm clue ComplexHeatmap dplyr dynamicTreeCut emdbook forestplot ggplot2 lpSolve matrixStats mclust pbapply plyr RColorBrewer rlang S4Vectors scater SingleCellExperiment smurf SummarizedExperiment]; };
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alevinQC = derive2 { name="alevinQC"; version="1.12.0"; sha256="0g8ifinrqzncpw55ik2pz2l52fp5dkai2ghwfz1wwd2qn4x88zrv"; depends=[cowplot dplyr DT GGally ggplot2 Rcpp rjson rlang rmarkdown shiny shinydashboard tximport]; };
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alevinQC = derive2 { name="alevinQC"; version="1.12.1"; sha256="0g75qnz7ah0widdjn99lhvnacz38vgl9j86n65wyswsf413hz3bb"; depends=[cowplot dplyr DT GGally ggplot2 Rcpp rjson rlang rmarkdown shiny shinydashboard tximport]; };
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alpine = derive2 { name="alpine"; version="1.22.0"; sha256="1nl1hxwakh5m9rqm3ksn2jzknsj9xnwl51bmc30knknm4q35wdv9"; depends=[Biostrings GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges graph IRanges RBGL Rsamtools S4Vectors speedglm stringr SummarizedExperiment]; };
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altcdfenvs = derive2 { name="altcdfenvs"; version="2.58.0"; sha256="0caw9h0gw3qfrg4iqrydjdbagm059if513qjp1869cb0cq1w45r6"; depends=[affy Biobase BiocGenerics Biostrings hypergraph makecdfenv S4Vectors]; };
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amplican = derive2 { name="amplican"; version="1.18.0"; sha256="0q1c0g93xl0s2i6b1g21s11dngh7fbz63sn48yfiasvpxxlbag5q"; depends=[BiocGenerics BiocParallel Biostrings clusterCrit data_table dplyr GenomeInfoDb GenomicRanges ggplot2 ggthemes gridExtra gtable IRanges knitr Matrix matrixStats Rcpp rmarkdown S4Vectors ShortRead stringr waffle]; };
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@ -1103,7 +1103,7 @@ in with self; {
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basecallQC = derive2 { name="basecallQC"; version="1.20.0"; sha256="07mcg0bs13apabhsip997nj6riqdrv9247azg379z6anaa0b0vpd"; depends=[data_table dplyr DT ggplot2 knitr lazyeval magrittr prettydoc raster rmarkdown ShortRead stringr tidyr XML yaml]; };
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basilisk = derive2 { name="basilisk"; version="1.8.0"; sha256="1p90wq8a9wrpqpgmcy4zgh5skdw65gg2gsb3lnx78zk9khq0yyzh"; depends=[basilisk_utils dir_expiry reticulate]; };
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basilisk_utils = derive2 { name="basilisk.utils"; version="1.8.0"; sha256="1jnqv0rlljkq27rd4ixl763v335f2aanm4fzr386yc81fj4vnmhk"; depends=[dir_expiry]; };
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batchelor = derive2 { name="batchelor"; version="1.12.0"; sha256="0mncnz1lfzj8si9s52z5k80vahx1m0abb6lrfwsnd7psmz5ddnhp"; depends=[beachmat BiocGenerics BiocNeighbors BiocParallel BiocSingular DelayedArray DelayedMatrixStats igraph Matrix Rcpp ResidualMatrix S4Vectors ScaledMatrix scuttle SingleCellExperiment SummarizedExperiment]; };
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batchelor = derive2 { name="batchelor"; version="1.12.3"; sha256="00ix3hvhgalxg63qnynv2waa273jk336lg47k72qwxfzimsxfjxc"; depends=[beachmat BiocGenerics BiocNeighbors BiocParallel BiocSingular DelayedArray DelayedMatrixStats igraph Matrix Rcpp ResidualMatrix S4Vectors ScaledMatrix scuttle SingleCellExperiment SummarizedExperiment]; };
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bayNorm = derive2 { name="bayNorm"; version="1.14.0"; sha256="12896sryq5bfbqglpk3dg9cdsq6rk3jhzdqcpyasvk6w7v1w8bin"; depends=[BB BiocParallel doSNOW fitdistrplus foreach iterators locfit MASS Matrix Rcpp RcppArmadillo RcppProgress SingleCellExperiment SummarizedExperiment]; };
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baySeq = derive2 { name="baySeq"; version="2.30.0"; sha256="1yqykndyv32s2rk7x86qf410qr0pigc8z4gdkl8vhj4dgyr47n2j"; depends=[abind edgeR GenomicRanges]; };
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bcSeq = derive2 { name="bcSeq"; version="1.18.0"; sha256="0bn3maqxayprrd73gwvxgqkk0zqc0nanw29wsnmvw7z1bd15zqy0"; depends=[Biostrings Matrix Rcpp]; };
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@ -1136,7 +1136,7 @@ in with self; {
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biomaRt = derive2 { name="biomaRt"; version="2.52.0"; sha256="0yn3kanyrplc89a900xiz33nw1v23mkljvd5isizgs8gzvwzf8xg"; depends=[AnnotationDbi BiocFileCache digest httr progress rappdirs stringr XML xml2]; };
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biomformat = derive2 { name="biomformat"; version="1.24.0"; sha256="12wqjipxhngmlnrdmx329dqmkmy2wa4nkkrhwaqv2nwy90dncs9n"; depends=[jsonlite Matrix plyr rhdf5]; };
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biomvRCNS = derive2 { name="biomvRCNS"; version="1.36.0"; sha256="0i576g7pkivqaxff1pkb760mdpx8v9fh071aic1mwfnlfa7k87ln"; depends=[GenomicRanges Gviz IRanges mvtnorm]; };
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biosigner = derive2 { name="biosigner"; version="1.24.0"; sha256="11w28nlz0f06idbna5k9xs891w516401l1zab5gg7s0z3xxaki4f"; depends=[Biobase e1071 MultiDataSet randomForest ropls]; };
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biosigner = derive2 { name="biosigner"; version="1.24.2"; sha256="0vdv2by3qv7y8vzr8qgg7apwwgsa0fhlfrhzns7g3nas7883c89m"; depends=[Biobase e1071 MultiAssayExperiment MultiDataSet randomForest ropls SummarizedExperiment]; };
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biotmle = derive2 { name="biotmle"; version="1.20.0"; sha256="1frig90krvfdk6nwpmslpj0pvligyzwzfwwci7hzwcmbglk5jj22"; depends=[assertthat BiocGenerics BiocParallel dplyr drtmle ggplot2 ggsci limma S4Vectors SummarizedExperiment superheat tibble]; };
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biovizBase = derive2 { name="biovizBase"; version="1.44.0"; sha256="1ffzf7yvl47l8v8a50m8g9q33hgwvxg4fcm8ld2yy8hd2zl86zyd"; depends=[AnnotationDbi AnnotationFilter BiocGenerics Biostrings dichromat ensembldb GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges Hmisc IRanges RColorBrewer rlang Rsamtools S4Vectors scales SummarizedExperiment VariantAnnotation]; };
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biscuiteer = derive2 { name="biscuiteer"; version="1.10.0"; sha256="0y7vbdaafiga16yr0d22w1v4p0jmczndcar0r0km06f5y1b74amr"; depends=[Biobase BiocGenerics BiocParallel biscuiteerData bsseq data_table DelayedMatrixStats dmrseq GenomeInfoDb GenomicRanges gtools HDF5Array Homo_sapiens impute IRanges Matrix matrixStats Mus_musculus QDNAseq qualV R_utils readr Rsamtools rtracklayer S4Vectors SummarizedExperiment VariantAnnotation]; };
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@ -1145,7 +1145,7 @@ in with self; {
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bluster = derive2 { name="bluster"; version="1.6.0"; sha256="1g496yc7mdhshf6r0n8xhj7ax936ia5z2cx72lqyk2vzzzl5c4v8"; depends=[BiocNeighbors BiocParallel cluster igraph Matrix Rcpp S4Vectors]; };
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bnbc = derive2 { name="bnbc"; version="1.18.0"; sha256="1d2m98vpjl2ibzx61rr9a95v7wa5zz2s2bnymwmm08445dv33sy2"; depends=[BiocGenerics data_table EBImage GenomeInfoDb GenomicRanges IRanges matrixStats preprocessCore Rcpp rhdf5 S4Vectors SummarizedExperiment sva]; };
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bnem = derive2 { name="bnem"; version="1.4.0"; sha256="1qh3kxy09q29s9sg17gg3yhvcq3p99mnvr6zm91izf8fgyivz912"; depends=[affy binom Biobase CellNOptR cluster epiNEM flexclust graph limma matrixStats mnem RColorBrewer Rgraphviz rmarkdown snowfall sva vsn]; };
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borealis = derive2 { name="borealis"; version="1.0.0"; sha256="0awcb7m56yzyglpxlbyvcg3l5cvsmrrlsdybmdyfla8qljz46rhc"; depends=[Biobase bsseq cowplot doMC dplyr DSS foreach gamlss gamlss_dist GenomicRanges ggplot2 plyr purrr R_utils rlang]; };
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borealis = derive2 { name="borealis"; version="1.0.1"; sha256="0glldfg1h480fpm5wpsqq6mffnkwvfknpl2hdvxvwnarqv0qiz7s"; depends=[Biobase bsseq cowplot doParallel dplyr DSS foreach gamlss gamlss_dist GenomicRanges ggplot2 plyr purrr R_utils rlang snow]; };
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brainflowprobes = derive2 { name="brainflowprobes"; version="1.10.0"; sha256="0vyzw4i28bz15z06rz57h1ipcxs5lqlwcpf58a1wz0gzn5na11js"; depends=[Biostrings BSgenome_Hsapiens_UCSC_hg19 bumphunter cowplot derfinder derfinderPlot GenomicRanges GenomicState ggplot2 RColorBrewer]; };
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branchpointer = derive2 { name="branchpointer"; version="1.22.0"; sha256="0rsfx60l6972nz4kpjly0h4sm48flfrwskgh1shl3hbq3bnli18b"; depends=[biomaRt Biostrings BSgenome_Hsapiens_UCSC_hg38 caret cowplot data_table gbm GenomeInfoDb GenomicRanges ggplot2 IRanges kernlab plyr rtracklayer S4Vectors stringr]; };
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breakpointR = derive2 { name="breakpointR"; version="1.14.0"; sha256="0mx8lk8q69jq5wqwhp7qvqv1zvm3hj6z53z3sil0470ri7jdyh6l"; depends=[BiocGenerics breakpointRdata cowplot doParallel foreach GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 gtools IRanges Rsamtools S4Vectors]; };
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@ -1154,7 +1154,7 @@ in with self; {
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bsseq = derive2 { name="bsseq"; version="1.32.0"; sha256="1jpfib2vb6hd7pgh3d33jgch24lba175zmbalwsbgvlmmyyf1ki5"; depends=[beachmat Biobase BiocGenerics BiocParallel Biostrings BSgenome data_table DelayedArray DelayedMatrixStats GenomeInfoDb GenomicRanges gtools HDF5Array IRanges limma locfit permute R_utils Rcpp rhdf5 S4Vectors scales SummarizedExperiment]; };
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bugsigdbr = derive2 { name="bugsigdbr"; version="1.2.0"; sha256="1ib6aq0c07bjazh0clvn2nqx0vwpf1srp354rr162r37cix7mxlr"; depends=[BiocFileCache vroom]; };
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bumphunter = derive2 { name="bumphunter"; version="1.38.0"; sha256="0k92ps9chqsimbc7vsr8swg679zfv8nfn5zahbqq4nknhhy7hwxw"; depends=[AnnotationDbi BiocGenerics doRNG foreach GenomeInfoDb GenomicFeatures GenomicRanges IRanges iterators limma locfit matrixStats S4Vectors]; };
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cBioPortalData = derive2 { name="cBioPortalData"; version="2.8.0"; sha256="05nnj18bsxvxrghb8m3bb7z9w3wj3ijcgbqw0vsbszmhj9xhr5ja"; depends=[AnVIL BiocFileCache digest dplyr GenomeInfoDb GenomicRanges httr IRanges MultiAssayExperiment RaggedExperiment readr RTCGAToolbox S4Vectors SummarizedExperiment TCGAutils tibble tidyr]; };
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cBioPortalData = derive2 { name="cBioPortalData"; version="2.8.2"; sha256="09bjlyr4l7iifgk39kkn3bq9lddvsgg2qj362xxy6z8igzblm05x"; depends=[AnVIL BiocFileCache digest dplyr GenomeInfoDb GenomicRanges httr IRanges MultiAssayExperiment RaggedExperiment readr RTCGAToolbox S4Vectors SummarizedExperiment TCGAutils tibble tidyr]; };
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cTRAP = derive2 { name="cTRAP"; version="1.14.0"; sha256="13mkdc1fpik9wpcviil0m0ph9cr69b1isdwb8nwaszlhkb1spmas"; depends=[AnnotationDbi AnnotationHub binr cowplot data_table dplyr DT fastmatch fgsea ggplot2 ggrepel highcharter htmltools httr limma pbapply purrr qs R_utils readxl reshape2 rhdf5 rlang scales shiny shinycssloaders tibble]; };
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caOmicsV = derive2 { name="caOmicsV"; version="1.25.0"; sha256="10i4imjihmssdwfys21fsqng8zfp7sxzkc58m8qmnh6s5sccb3sz"; depends=[bc3net igraph]; };
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cageminer = derive2 { name="cageminer"; version="1.2.0"; sha256="04lmabxv3hgxd4b52qg7rbi01jsd18hi9dwi3i63si7073ij5ni7"; depends=[BioNERO GenomeInfoDb GenomicRanges ggbio ggplot2 ggtext IRanges reshape2]; };
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@ -1163,7 +1163,7 @@ in with self; {
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cancerclass = derive2 { name="cancerclass"; version="1.40.0"; sha256="1s80w8ksf735ps677c7dcwkkpq1ynjqmp2r4biqav4j1y50nbi57"; depends=[binom Biobase]; };
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casper = derive2 { name="casper"; version="2.30.0"; sha256="0rx23ppj78m7dinvrim3hdh330xdlv2yw5405akd32dxr5dhp0wh"; depends=[Biobase BiocGenerics coda EBarrays gaga GenomeInfoDb GenomicFeatures GenomicRanges gtools IRanges limma mgcv Rsamtools rtracklayer S4Vectors sqldf survival VGAM]; };
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categoryCompare = derive2 { name="categoryCompare"; version="1.40.0"; sha256="1bidg957kjfg16w07gdbb8ygzipg2c47by9wilj4ijm32czv2ls7"; depends=[annotate AnnotationDbi Biobase BiocGenerics Category colorspace GOstats graph GSEABase hwriter RCy3]; };
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cbaf = derive2 { name="cbaf"; version="1.18.0"; sha256="1cl2gchmsarfn2j88nmjd1528dldhn0wb3dvavf3lxdgy90b0466"; depends=[BiocFileCache cBioPortalData genefilter gplots openxlsx RColorBrewer]; };
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cbaf = derive2 { name="cbaf"; version="1.18.1"; sha256="1bhn2iajvpd0r6vsd4dbf5i2h98pwn878dj26inmfkpdrlmk035x"; depends=[BiocFileCache cBioPortalData genefilter gplots openxlsx RColorBrewer]; };
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cbpManager = derive2 { name="cbpManager"; version="1.4.0"; sha256="0h60a4cx3cgzbs9mchdasy7vgh6rm8vqp5w770328jwq9wyj3xkr"; depends=[basilisk dplyr DT htmltools jsonlite magrittr markdown plyr rapportools reticulate rintrojs shiny shinyBS shinycssloaders shinydashboard vroom]; };
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ccfindR = derive2 { name="ccfindR"; version="1.16.0"; sha256="1gg5508qxhv0g4k3m1iy3bzs53wlqbvnx3lsm77zmxhng38zzniv"; depends=[ape gtools irlba Matrix RColorBrewer Rcpp RcppEigen Rdpack Rmpi Rtsne S4Vectors SingleCellExperiment SummarizedExperiment]; };
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ccmap = derive2 { name="ccmap"; version="1.22.0"; sha256="03rw2k0ln1lr4c0sz06x1b8wyriq659bvngbb9wyr4mkcbjz5jy7"; depends=[AnnotationDbi BiocManager ccdata data_table doParallel foreach lsa xgboost]; };
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@ -1173,7 +1173,7 @@ in with self; {
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celda = derive2 { name="celda"; version="1.12.0"; sha256="1qqm4pags5bp08w70419qlaghfr3r3pmb870k8ax9snbiqx32sp3"; depends=[circlize ComplexHeatmap data_table dbscan DelayedArray digest doParallel enrichR foreach ggplot2 ggrepel gtable Matrix matrixStats MCMCprecision multipanelfigure plyr RColorBrewer Rcpp RcppEigen reshape2 Rtsne S4Vectors scales scater scran SingleCellExperiment stringr SummarizedExperiment uwot withr]; };
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cellHTS2 = derive2 { name="cellHTS2"; version="2.60.0"; sha256="1mrf7mdhcbvvcizc8nr8mr6xp6k9zv6v97p3zz173iqhlwf0mvvn"; depends=[Biobase BiocGenerics Category genefilter GSEABase hwriter locfit RColorBrewer splots vsn]; };
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cellTree = derive2 { name="cellTree"; version="1.26.0"; sha256="0zpf05w4bcnjfzb8jqq936rs5ji84gpn72bndsk6ipg8s4lh0bav"; depends=[gplots igraph maptpx slam topGO topicmodels xtable]; };
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cellbaseR = derive2 { name="cellbaseR"; version="1.20.0"; sha256="0jk6ynq6h9xxwd8jlm5d2afb4kibkrh5212az4if175rn557wz6r"; depends=[BiocParallel data_table doParallel foreach httr jsonlite pbapply R_utils Rsamtools tidyr]; };
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cellbaseR = derive2 { name="cellbaseR"; version="1.20.1"; sha256="15y11jykxm3c681lr277zvzwsfbz0rxfzmdwanlmh0akafyl6nr6"; depends=[BiocParallel data_table doParallel foreach httr jsonlite pbapply R_utils Rsamtools tidyr]; };
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cellity = derive2 { name="cellity"; version="1.24.0"; sha256="0ywghrfj6m6hcz9yvpq0ww3p05rxdrfjna7il9faa76va5m8ssly"; depends=[AnnotationDbi e1071 ggplot2 mvoutlier org_Hs_eg_db org_Mm_eg_db robustbase topGO]; };
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cellmigRation = derive2 { name="cellmigRation"; version="1.4.0"; sha256="09c6rmraajiqx7hgxmjyx4h32gdjy849ymyid0zvxqq4cfrx0pbs"; depends=[doParallel FactoMineR FME foreach Hmisc matrixStats reshape2 sp SpatialTools tiff vioplot]; };
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cellscape = derive2 { name="cellscape"; version="1.20.0"; sha256="1k0z7sw4d3wxy4sz42b6aplq2njm673sfqgzzyf6m8iax2rvgvhs"; depends=[dplyr gtools htmlwidgets jsonlite plyr reshape2 stringr]; };
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@ -1204,7 +1204,7 @@ in with self; {
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clstutils = derive2 { name="clstutils"; version="1.44.0"; sha256="0w2gki24xf9m8qh1289hns8bkr7gj6big21lyb4p2mp652z1daw7"; depends=[ape clst lattice rjson RSQLite]; };
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clustComp = derive2 { name="clustComp"; version="1.24.0"; sha256="1svj1xvg8cn1hm5snw8yv764382vc41m7q2qjwv7cfyv7ri3ai42"; depends=[sm]; };
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clusterExperiment = derive2 { name="clusterExperiment"; version="2.16.0"; sha256="1xd2kxmdg51hhj0zvz7pxmpdvb1sya7prsf9ny2wj2y8ivrqgn4f"; depends=[ape BiocGenerics BiocSingular cluster DelayedArray edgeR HDF5Array howmany kernlab limma locfdr Matrix matrixStats mbkmeans NMF phylobase pracma RColorBrewer Rcpp S4Vectors scales SingleCellExperiment stringr SummarizedExperiment zinbwave]; };
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clusterProfiler = derive2 { name="clusterProfiler"; version="4.4.1"; sha256="03bg3agisrm4q10gg57dksvd1ws37if6a1gwcxaybb4c50zadm8p"; depends=[AnnotationDbi DOSE downloader dplyr enrichplot GO_db GOSemSim magrittr plyr qvalue rlang tidyr yulab_utils]; };
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clusterProfiler = derive2 { name="clusterProfiler"; version="4.4.4"; sha256="0k5jhry0j6wa7779n3hrw4ld4bvyahpgpbwi2a0g704m3dd3mqp5"; depends=[AnnotationDbi DOSE downloader dplyr enrichplot GO_db GOSemSim magrittr plyr qvalue rlang tidyr yulab_utils]; };
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clusterSeq = derive2 { name="clusterSeq"; version="1.20.0"; sha256="0rh9ql3f1z79hxwlnsv5r8l0cpqyr6jxlz38f1aakshdlwdxlkiq"; depends=[baySeq BiocGenerics BiocParallel]; };
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clusterStab = derive2 { name="clusterStab"; version="1.68.0"; sha256="0p5dk9s3zrd5d2ap5i445jlkhjp7f8vh3dj3h59wya2n4phpigb4"; depends=[Biobase]; };
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clustifyr = derive2 { name="clustifyr"; version="1.8.0"; sha256="1c1lbgsmwafg9aa8j95x235270axp1g7mq41hmidc9mf4f6vclxc"; depends=[cowplot dplyr entropy fgsea ggplot2 httr Matrix matrixStats proxy readr rlang S4Vectors scales SingleCellExperiment stringr SummarizedExperiment tibble tidyr]; };
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@ -1213,7 +1213,7 @@ in with self; {
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cn_mops = derive2 { name="cn.mops"; version="1.42.0"; sha256="152l9nnncyyz182cnafw8ipy94jf7mizhr6xmvp3l4qj9yixr0y5"; depends=[Biobase BiocGenerics exomeCopy GenomeInfoDb GenomicRanges IRanges Rsamtools S4Vectors]; };
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cnvGSA = derive2 { name="cnvGSA"; version="1.40.0"; sha256="0wvkn62i4g3r5fg7am6mmwri01gr5g5dil5mp5w4na57h1svsksc"; depends=[brglm doParallel foreach GenomicRanges splitstackshape]; };
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coGPS = derive2 { name="coGPS"; version="1.40.0"; sha256="1211fvcf6li32575p8638a6hf4a6bqqkx4jyfb8hpymhj5d4z5lx"; depends=[]; };
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coMET = derive2 { name="coMET"; version="1.28.0"; sha256="03b7a1b0g3zrh34ifjrylqdd1yi033lda6q71mir6plqr9y7fva1"; depends=[biomaRt colortools corrplot GenomicRanges gridExtra Gviz hash IRanges psych rtracklayer S4Vectors]; };
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coMET = derive2 { name="coMET"; version="1.28.0"; sha256="03b7a1b0g3zrh34ifjrylqdd1yi033lda6q71mir6plqr9y7fva1"; depends=[biomaRt corrplot GenomicRanges gridExtra Gviz hash IRanges psych rtracklayer S4Vectors]; };
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coMethDMR = derive2 { name="coMethDMR"; version="1.0.0"; sha256="0n89jv29mqrc2qjn7fv7zcn1ycsfrlsfs5ps1yiw5p77mq2rapp4"; depends=[AnnotationHub BiocParallel bumphunter ExperimentHub GenomicRanges IRanges lmerTest]; };
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coRdon = derive2 { name="coRdon"; version="1.14.0"; sha256="1kiw6kbbwqmr89mzppmgral0zxd5shmp53xyvbcr26fxs0xn1np2"; depends=[Biobase Biostrings data_table dplyr ggplot2 purrr stringr]; };
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codelink = derive2 { name="codelink"; version="1.64.0"; sha256="0r1srzx7z2833yvbnmdmbpkhy7irs4hdy2901bzqcwp91b4n6q75"; depends=[annotate Biobase BiocGenerics limma]; };
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@ -1251,8 +1251,8 @@ in with self; {
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crisprScore = derive2 { name="crisprScore"; version="1.0.0"; sha256="19vwvjq7pw6m813saldns38y3rhg7a63f5cd5sly3qiai8qfa3bb"; depends=[basilisk BiocGenerics Biostrings crisprScoreData IRanges randomForest reticulate stringr XVector]; };
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crisprseekplus = derive2 { name="crisprseekplus"; version="1.22.0"; sha256="18xiwjbssyz7dphiafqza5awxb6b4g023r3lq51mggbqczhrqwfp"; depends=[AnnotationDbi BiocManager BSgenome CRISPRseek DT GenomicFeatures GenomicRanges GUIDEseq hash shiny shinyjs]; };
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crlmm = derive2 { name="crlmm"; version="1.54.0"; sha256="0znspkc8mvfq94687dzmzix1dnnz32nvv2pdhv9cay2q6sv3d6z5"; depends=[affyio beanplot Biobase BiocGenerics ellipse ff foreach illuminaio lattice limma matrixStats mvtnorm oligoClasses preprocessCore RcppEigen VGAM]; };
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crossmeta = derive2 { name="crossmeta"; version="1.22.0"; sha256="03mlyz6bdzbbbb9fznlbc8d0yzcq1jbqlx7x25lkcf2bvrqfbbxf"; depends=[affxparser affy AnnotationDbi Biobase BiocGenerics BiocManager data_table DBI DT edgeR fdrtool GEOquery limma matrixStats metaMA miniUI oligo RCurl reader readxl RSQLite shiny shinyBS shinyjs shinypanel shinyWidgets stringr sva tibble XML]; };
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csaw = derive2 { name="csaw"; version="1.30.0"; sha256="0hjfli504kn4mfh51p8aqd4g27fjxf2jjlpy149fb5ff79nfllgd"; depends=[BiocGenerics BiocParallel edgeR GenomeInfoDb GenomicRanges IRanges limma Matrix metapod Rcpp Rhtslib Rsamtools S4Vectors SummarizedExperiment zlibbioc]; };
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crossmeta = derive2 { name="crossmeta"; version="1.22.1"; sha256="1qqbs11b5srm063igwddgnkmk65fsi7zy3ncl80q0bikn9d9dbcs"; depends=[affxparser affy AnnotationDbi Biobase BiocGenerics BiocManager data_table DBI DT edgeR fdrtool GEOquery limma matrixStats metaMA miniUI oligo RCurl reader readxl RSQLite shiny shinyBS shinyjs shinypanel shinyWidgets stringr sva tibble XML]; };
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csaw = derive2 { name="csaw"; version="1.30.1"; sha256="12fyrg251g0c25vff3badi3mrw6lwhlxnq1xc9q5m1mq9p6151d3"; depends=[BiocGenerics BiocParallel edgeR GenomeInfoDb GenomicRanges IRanges limma Matrix metapod Rcpp Rhtslib Rsamtools S4Vectors SummarizedExperiment zlibbioc]; };
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csdR = derive2 { name="csdR"; version="1.2.0"; sha256="02r3waqvv4v7pjbw2xv41y46ammlm5s04hg0pwpb327ia6pz9c1v"; depends=[glue matrixStats Rcpp RhpcBLASctl WGCNA]; };
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ctc = derive2 { name="ctc"; version="1.70.0"; sha256="0c9pgp25dqx12fmi4cqm7xyxjmy6g7wv9vbljgdjghaij2lrc4pb"; depends=[amap]; };
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ctgGEM = derive2 { name="ctgGEM"; version="1.7.0"; sha256="0hmapz96r024r3bws1wf0spd0i81viyma859y9nn93jrwxscrcdb"; depends=[Biobase BiocGenerics igraph Matrix monocle sincell SummarizedExperiment TSCAN]; };
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@ -1274,7 +1274,7 @@ in with self; {
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dasper = derive2 { name="dasper"; version="1.6.0"; sha256="0cv51fkmi29cnba750fkayycfgsn93wh5xll0m5rjpqz7lxzc83s"; depends=[basilisk BiocFileCache BiocParallel data_table dplyr GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 ggpubr ggrepel IRanges magrittr megadepth plyranges readr reticulate rtracklayer S4Vectors stringr SummarizedExperiment tidyr]; };
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dcGSA = derive2 { name="dcGSA"; version="1.24.0"; sha256="1p0i81bh6knkyy0d86icsa4dcdx0mahhdgcg3fyqnzn6bhwhk3bg"; depends=[BiocParallel Matrix]; };
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dcanr = derive2 { name="dcanr"; version="1.12.0"; sha256="0c4x3b8azcrqlkhbs7db4qh7828yx311bx1bng6wy7121asni4kz"; depends=[circlize doRNG foreach igraph Matrix plyr RColorBrewer reshape2 stringr]; };
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dce = derive2 { name="dce"; version="1.4.0"; sha256="14sapfhbjy3cx4knnxjlskraf8ky2k6akg4vk4z1a6afxcfw7qc8"; depends=[assertthat CombinePValue dplyr edgeR epiNEM expm ggplot2 ggraph glm2 glue graph graphite harmonicmeanp igraph logger magrittr MASS Matrix metap mnem naturalsort org_Hs_eg_db pcalg ppcor purrr reshape2 Rgraphviz rlang shadowtext tidygraph tidyverse]; };
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dce = derive2 { name="dce"; version="1.4.0"; sha256="14sapfhbjy3cx4knnxjlskraf8ky2k6akg4vk4z1a6afxcfw7qc8"; depends=[assertthat dplyr edgeR epiNEM expm ggplot2 ggraph glm2 glue graph graphite harmonicmeanp igraph logger magrittr MASS Matrix metap mnem naturalsort org_Hs_eg_db pcalg ppcor purrr reshape2 Rgraphviz rlang shadowtext tidygraph tidyverse]; };
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ddCt = derive2 { name="ddCt"; version="1.52.0"; sha256="03vgihxh8k33vdd1g96iwy69lf9zl3rg2bn0zdnbhrj7rfiqvj3q"; depends=[Biobase BiocGenerics lattice RColorBrewer xtable]; };
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ddPCRclust = derive2 { name="ddPCRclust"; version="1.16.0"; sha256="0pfscgbc241if2bj1xsj56nxcd31qq0wm39daznnjk155j5bfmx4"; depends=[clue flowCore flowDensity flowPeaks ggplot2 openxlsx plotrix R_utils SamSPECTRAL]; };
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dearseq = derive2 { name="dearseq"; version="1.8.1"; sha256="1f144k5gsclcmsnlsbisr2mivk91dbkci83wx1kznw6i15p4cpj1"; depends=[CompQuadForm dplyr ggplot2 KernSmooth magrittr matrixStats patchwork pbapply reshape2 rlang statmod survey tibble viridisLite]; };
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@ -1284,8 +1284,8 @@ in with self; {
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decompTumor2Sig = derive2 { name="decompTumor2Sig"; version="2.12.0"; sha256="04hg9bbga2s8scjxfd8wjlmr45nzzvh8d6gr0w929sybx4nj2qz6"; depends=[BiocGenerics Biostrings BSgenome_Hsapiens_UCSC_hg19 data_table GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 ggseqlogo gridExtra Matrix plyr quadprog readxl S4Vectors SummarizedExperiment TxDb_Hsapiens_UCSC_hg19_knownGene VariantAnnotation]; };
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decontam = derive2 { name="decontam"; version="1.16.0"; sha256="1g9hcfcfnpq6z21069yw0pyzncwznmvxb2xalg4y6y1604dy98q9"; depends=[ggplot2 reshape2]; };
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deconvR = derive2 { name="deconvR"; version="1.2.0"; sha256="091z3lncamscsvzj63zzbw7dr7vnkn0jwfkm5ljq4112w4rxgrm3"; depends=[assertthat BiocGenerics data_table dplyr e1071 foreach GenomicRanges IRanges magrittr MASS matrixStats methylKit nnls quadprog rsq S4Vectors tidyr]; };
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decoupleR = derive2 { name="decoupleR"; version="2.2.0"; sha256="0idsnhgi9xllkc8a9k8inl7pmqsz7z32cwsbkfwplakclg4bwad4"; depends=[broom dplyr magrittr Matrix purrr rlang stringr tibble tidyr tidyselect withr]; };
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deepSNV = derive2 { name="deepSNV"; version="1.42.0"; sha256="0si1x2bi5pff1dicpqg7hv4ziq46vm7lic72724ljsclpz9bfv6q"; depends=[Biostrings GenomicRanges IRanges Rhtslib SummarizedExperiment VariantAnnotation VGAM]; };
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decoupleR = derive2 { name="decoupleR"; version="2.2.2"; sha256="0q1w8yw3bwx8ai5z8rw8lz97w4cplxijq93634hza2vgkig1ck9m"; depends=[broom dplyr magrittr Matrix purrr rlang stringr tibble tidyr tidyselect withr]; };
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deepSNV = derive2 { name="deepSNV"; version="1.42.1"; sha256="0bgj1grv3a5bqhcdsw445x49kl3pz367svy6fnrzfsk9bmj46kgn"; depends=[Biostrings GenomicRanges IRanges Rhtslib SummarizedExperiment VariantAnnotation VGAM]; };
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deltaCaptureC = derive2 { name="deltaCaptureC"; version="1.10.0"; sha256="1v15v7lhxaymj2940k11z5bg5zpqsgncdpc4sxw8ff89m1ilwrlk"; depends=[DESeq2 GenomicRanges ggplot2 IRanges SummarizedExperiment tictoc]; };
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deltaGseg = derive2 { name="deltaGseg"; version="1.36.0"; sha256="1a2p4mx88n2hrg30gkilhisjf1hbnjqqv86hcji2ypz54axx7jdv"; depends=[changepoint fBasics ggplot2 pvclust reshape scales tseries wavethresh]; };
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densvis = derive2 { name="densvis"; version="1.6.0"; sha256="1w9j4gjk18mmfazl0rzma4mgwgg8s0rawxmyv4jysmdwirfr7jpl"; depends=[assertthat basilisk Rcpp reticulate]; };
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@ -1304,7 +1304,7 @@ in with self; {
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dir_expiry = derive2 { name="dir.expiry"; version="1.4.0"; sha256="098wzm8hlpy70c99k2sl4k8z2dllhw7rwdj8dhcskr7kaw71k3sq"; depends=[filelock]; };
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discordant = derive2 { name="discordant"; version="1.20.0"; sha256="0896ch07zpbwif48nz9n91gzsdkf7ax68vylhlfvz5mbgdd1cc3f"; depends=[Biobase biwt dplyr gtools MASS Rcpp]; };
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distinct = derive2 { name="distinct"; version="1.8.0"; sha256="0g7591km80zz1jhy5d8ys9snmva79prx2v4sdm57whn93mxqyp0l"; depends=[doParallel doRNG foreach ggplot2 limma Matrix Rcpp RcppArmadillo Rfast scater SingleCellExperiment SummarizedExperiment]; };
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dittoSeq = derive2 { name="dittoSeq"; version="1.8.0"; sha256="1mjsci1vcnsz3w1i693vmnmhjdz10lm7d4qyvxdg202mk75gzv2r"; depends=[colorspace cowplot ggplot2 ggrepel ggridges gridExtra pheatmap reshape2 S4Vectors SingleCellExperiment SummarizedExperiment]; };
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dittoSeq = derive2 { name="dittoSeq"; version="1.8.1"; sha256="0vi0hcyffaxp6yxsrq95bdlrhr85dvbqm9c7rg6a6blkfgwhlzb4"; depends=[colorspace cowplot ggplot2 ggrepel ggridges gridExtra pheatmap reshape2 S4Vectors SingleCellExperiment SummarizedExperiment]; };
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divergence = derive2 { name="divergence"; version="1.12.0"; sha256="0zh38cl5rsi7mx9nijhz8qrbjgfzrc4hgkcyywxady315zxfbl7y"; depends=[SummarizedExperiment]; };
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dks = derive2 { name="dks"; version="1.42.0"; sha256="1ljxin1c36glri7cq5mgw929gaivdakqhssdyblciy4y8qpkxa3s"; depends=[cubature]; };
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dmrseq = derive2 { name="dmrseq"; version="1.16.0"; sha256="1c99l62fi26bnbvpzrlsvvs722za0l5vfhddcrhzzzasabhccb4n"; depends=[AnnotationHub annotatr BiocParallel bsseq bumphunter DelayedMatrixStats GenomeInfoDb GenomicRanges ggplot2 IRanges locfit matrixStats nlme outliers RColorBrewer rtracklayer S4Vectors]; };
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@ -1319,23 +1319,23 @@ in with self; {
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easyRNASeq = derive2 { name="easyRNASeq"; version="2.32.0"; sha256="1dy1prn7qjvw7kjmq5cgdd0yvpw167f9m2azg1wxn2xfrdyb5ipr"; depends=[Biobase BiocFileCache BiocGenerics BiocParallel biomaRt Biostrings edgeR GenomeInfoDb genomeIntervals GenomicAlignments GenomicRanges IRanges locfit LSD rappdirs Rsamtools S4Vectors ShortRead SummarizedExperiment]; };
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easyreporting = derive2 { name="easyreporting"; version="1.8.0"; sha256="1jpgaa55zqnhqla0kid200c63ghwv0apm7p1g1z5ybrfxdlfrrkv"; depends=[rlang rmarkdown shiny]; };
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ecolitk = derive2 { name="ecolitk"; version="1.68.0"; sha256="07dax788x8p5dxwkw24hnlzkcpy72swzxl4ynhivjwixwy248diz"; depends=[Biobase]; };
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edge = derive2 { name="edge"; version="2.28.0"; sha256="1dld7pz3wwmfp4blnn6fh98dfybgw8b38vmydmfdrzim51p1h036"; depends=[Biobase jackstraw MASS qvalue snm sva]; };
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edgeR = derive2 { name="edgeR"; version="3.38.0"; sha256="17wbqbwaz8hvmpswj8869fjc410r0a5rfqqqw9jwlja9dn0h2agp"; depends=[limma locfit Rcpp]; };
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edge = derive2 { name="edge"; version="2.28.0"; sha256="1dld7pz3wwmfp4blnn6fh98dfybgw8b38vmydmfdrzim51p1h036"; depends=[Biobase MASS qvalue snm sva]; };
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edgeR = derive2 { name="edgeR"; version="3.38.1"; sha256="1q933m76155gy30wgps2gdd8pxzsfhppydjqn0fhjrwj6kqz8mik"; depends=[limma locfit Rcpp]; };
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eegc = derive2 { name="eegc"; version="1.22.0"; sha256="16ixc3bn5qkqy5w38428avzrd078xq5h2r8g0csms9b09hxmj65z"; depends=[AnnotationDbi clusterProfiler DESeq2 DOSE edgeR ggplot2 gplots igraph limma org_Hs_eg_db org_Mm_eg_db pheatmap R_utils S4Vectors sna wordcloud]; };
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eiR = derive2 { name="eiR"; version="1.36.0"; sha256="0pnv2cfdkagq31v2q7x9yfzi1q79nj76k1i0d92wzkxh8j2rnmhh"; depends=[BiocGenerics ChemmineR DBI digest RcppAnnoy RCurl RUnit snow snowfall]; };
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eisaR = derive2 { name="eisaR"; version="1.8.0"; sha256="1c1nmrc6xvmxk40wiwrqysvnslrfr318lypd6qbgh7h3z5n70s0w"; depends=[BiocGenerics edgeR GenomicRanges IRanges limma S4Vectors SummarizedExperiment]; };
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enhancerHomologSearch = derive2 { name="enhancerHomologSearch"; version="1.2.0"; sha256="06wycza921fqycwff7fbyjxp64p7lyqinjglvwgv9jk85pxm1dxp"; depends=[BiocFileCache BiocGenerics BiocParallel Biostrings BSgenome GenomeInfoDb GenomicRanges httr IRanges jsonlite Matrix motifmatchr Rcpp rtracklayer S4Vectors]; };
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enrichTF = derive2 { name="enrichTF"; version="1.12.0"; sha256="0fv50ma7jaqqbrzaznzvk6vza76if40f5vbxvl22s1ymk5chwk50"; depends=[BiocGenerics BSgenome clusterProfiler GenomeInfoDb GenomicRanges ggplot2 ggpubr heatmap3 IRanges JASPAR2018 magrittr motifmatchr pipeFrame R_utils rmarkdown rtracklayer S4Vectors TFBSTools]; };
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enrichplot = derive2 { name="enrichplot"; version="1.16.0"; sha256="0i6v9wr7m3m4lm9vdp2mq41kkd0r4gfi8yxvhg9bbq1m3vb5hfmm"; depends=[aplot DOSE ggplot2 ggraph ggtree GOSemSim igraph magrittr plyr purrr RColorBrewer reshape2 scatterpie shadowtext yulab_utils]; };
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enrichplot = derive2 { name="enrichplot"; version="1.16.1"; sha256="17ln1wbkq8sp7jw0dpkccj5qcsl382sgd7zic04dk99z9ag3mh02"; depends=[aplot DOSE ggplot2 ggraph ggtree GOSemSim igraph magrittr plyr purrr RColorBrewer reshape2 scatterpie shadowtext yulab_utils]; };
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ensemblVEP = derive2 { name="ensemblVEP"; version="1.37.1"; sha256="0r8khb8z99jm9dnk9b1q55q3nlk7q0hrxif4dzkcq4j27ddrhd8a"; depends=[BiocGenerics Biostrings GenomeInfoDb GenomicRanges S4Vectors SummarizedExperiment VariantAnnotation]; };
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ensembldb = derive2 { name="ensembldb"; version="2.20.1"; sha256="183rs74ngfvn9xz36csch495pqaash90yhhikm73m7b2bc37ziwz"; depends=[AnnotationDbi AnnotationFilter Biobase BiocGenerics Biostrings curl DBI GenomeInfoDb GenomicFeatures GenomicRanges IRanges ProtGenerics Rsamtools RSQLite rtracklayer S4Vectors]; };
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ensembldb = derive2 { name="ensembldb"; version="2.20.2"; sha256="12n21dcimdhgyjzk33m6xbv0m9ihgyzcf66vr1jr5ycv3rq2s7xc"; depends=[AnnotationDbi AnnotationFilter Biobase BiocGenerics Biostrings curl DBI GenomeInfoDb GenomicFeatures GenomicRanges IRanges ProtGenerics Rsamtools RSQLite rtracklayer S4Vectors]; };
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epiNEM = derive2 { name="epiNEM"; version="1.20.0"; sha256="1bi0pjmdvlvfjvl6m6r7hd3bd6jdh18i3bnk3s6vpnb52hi35a07"; depends=[BoolNet e1071 graph gtools igraph latex2exp lattice latticeExtra minet mnem pcalg RColorBrewer]; };
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epialleleR = derive2 { name="epialleleR"; version="1.4.0"; sha256="0qw2wvrbfin2l80id06pr779l1mkvlafadkl3ja4s4nmn2ip5yfn"; depends=[BH BiocGenerics data_table GenomeInfoDb GenomicRanges Rcpp Rhtslib stringi SummarizedExperiment VariantAnnotation zlibbioc]; };
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epidecodeR = derive2 { name="epidecodeR"; version="1.4.0"; sha256="1fingfn0rbygvlhkgva6999sw4xc8g7k6w8nm86vw3dz5c77mq5f"; depends=[dplyr EnvStats GenomicRanges ggplot2 ggpubr IRanges rstatix rtracklayer]; };
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epigenomix = derive2 { name="epigenomix"; version="1.36.0"; sha256="15drlib696rylc4952rjnxrc0hfn5nskap93sz6f98b9v1g9gsmk"; depends=[beadarray Biobase BiocGenerics GenomeInfoDb GenomicRanges IRanges MCMCpack Rsamtools S4Vectors SummarizedExperiment]; };
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epigraHMM = derive2 { name="epigraHMM"; version="1.4.0"; sha256="13cfc86yz7wvjm3mqnmmcqq0q01w35s4vwzjhvrkwck1yn4kkpf4"; depends=[bamsignals csaw data_table GenomeInfoDb GenomicRanges ggplot2 ggpubr GreyListChIP IRanges limma magrittr MASS Matrix pheatmap Rcpp RcppArmadillo rhdf5 Rhdf5lib Rsamtools rtracklayer S4Vectors scales SummarizedExperiment]; };
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epihet = derive2 { name="epihet"; version="1.12.0"; sha256="0v002h96b4p2sb30iszcvfvnzqm5dnw8klypmd0496zcr7dqk8jk"; depends=[data_table doParallel EntropyExplorer foreach GenomicRanges ggplot2 igraph IRanges pheatmap qvalue ReactomePA Rtsne S4Vectors WGCNA]; };
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epimutacions = derive2 { name="epimutacions"; version="1.0.0"; sha256="16gjqjqrbpsskrwp29pfw54ysv0p7755kvpcx9n4syzj8l1i0s2d"; depends=[BiocGenerics BiocParallel biomaRt bumphunter epimutacionsData GenomicFeatures GenomicRanges ggplot2 IRanges isotree matrixStats minfi robustbase S4Vectors SummarizedExperiment]; };
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epihet = derive2 { name="epihet"; version="1.12.0"; sha256="0v002h96b4p2sb30iszcvfvnzqm5dnw8klypmd0496zcr7dqk8jk"; depends=[data_table doParallel foreach GenomicRanges ggplot2 igraph IRanges pheatmap qvalue ReactomePA Rtsne S4Vectors WGCNA]; };
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epimutacions = derive2 { name="epimutacions"; version="1.0.3"; sha256="1ga5z7w5gimzzf0zhqv3ina7vhjkas0pngjmjxpgmpk4c5z6v76j"; depends=[BiocGenerics BiocParallel biomaRt bumphunter epimutacionsData GenomicFeatures GenomicRanges ggplot2 IRanges isotree matrixStats minfi robustbase S4Vectors SummarizedExperiment]; };
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epistack = derive2 { name="epistack"; version="1.2.0"; sha256="0vlxdl99y1hl6pzsc55khgw5r102vvlfqlm2d7z21vnvxr4dwijr"; depends=[BiocGenerics GenomicRanges IRanges plotrix S4Vectors SummarizedExperiment viridisLite]; };
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epivizr = derive2 { name="epivizr"; version="2.26.0"; sha256="1hzhx062qwfzg2fr61zzsnfzzkyn3z0i5b1pdxc99ba32qx1bphz"; depends=[bumphunter epivizrData epivizrServer GenomeInfoDb GenomicRanges IRanges S4Vectors]; };
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epivizrChart = derive2 { name="epivizrChart"; version="1.18.0"; sha256="0pyyypp75nbbxqcsid50r16qdhj280snl4jwbxqfjnqiyjh7wsrm"; depends=[BiocGenerics epivizrData epivizrServer htmltools rjson]; };
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@ -1350,13 +1350,13 @@ in with self; {
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eudysbiome = derive2 { name="eudysbiome"; version="1.26.0"; sha256="1pmk1x221hpds68yq2izwrfmvwd6v0gi0r40ggnlc9zrpx2s9fpm"; depends=[Biostrings plyr R_utils Rsamtools]; };
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evaluomeR = derive2 { name="evaluomeR"; version="1.12.0"; sha256="0wvha5ppx937b6qhxf95j0bwav07gq1bs2hw2q487mssksd7s1r2"; depends=[class cluster corrplot flexmix fpc ggdendro ggplot2 kableExtra MASS matrixStats mclust MultiAssayExperiment plotrix prabclus randomForest Rdpack reshape2 SummarizedExperiment]; };
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exomeCopy = derive2 { name="exomeCopy"; version="1.42.0"; sha256="0wfigjicbz22dijibbcz38j7javlj891q2f9mgwjpg6pwb0xi178"; depends=[GenomeInfoDb GenomicRanges IRanges Rsamtools]; };
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exomePeak2 = derive2 { name="exomePeak2"; version="1.8.0"; sha256="1m5vmmarsmils7l3vwhcgi5lb517054qbcyhl5bqc9jahbzmdxkj"; depends=[BiocGenerics BiocParallel Biostrings BSgenome DESeq2 GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 IRanges magrittr mclust Rsamtools rtracklayer S4Vectors speedglm SummarizedExperiment]; };
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extraChIPs = derive2 { name="extraChIPs"; version="1.0.0"; sha256="0g5bc8887gmr1i5314spq363wfsvqz7170jxr18yz7lbamyqyca0"; depends=[BiocIO BiocParallel broom csaw dplyr edgeR EnrichedHeatmap forcats GenomeInfoDb GenomicInteractions GenomicRanges ggplot2 ggrepel ggside glue Gviz InteractionSet IRanges limma RColorBrewer rlang Rsamtools rtracklayer S4Vectors scales scatterpie stringr SummarizedExperiment tibble tidyr tidyselect vctrs]; };
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exomePeak2 = derive2 { name="exomePeak2"; version="1.8.1"; sha256="1vr5sijfddzss96zw560i46dgjw5jwrmi5dbgqjvbrrrr371sbk2"; depends=[BiocGenerics BiocParallel Biostrings BSgenome DESeq2 GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 IRanges magrittr mclust Rsamtools rtracklayer S4Vectors speedglm SummarizedExperiment]; };
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extraChIPs = derive2 { name="extraChIPs"; version="1.0.1"; sha256="00sy4z5inmnyiymd453svd7hs0jgwbdc82fk2l92cayhm1q0i8qp"; depends=[BiocIO BiocParallel broom csaw dplyr edgeR EnrichedHeatmap forcats GenomeInfoDb GenomicInteractions GenomicRanges ggplot2 ggrepel ggside glue Gviz InteractionSet IRanges limma RColorBrewer rlang Rsamtools rtracklayer S4Vectors scales scatterpie stringr SummarizedExperiment tibble tidyr tidyselect vctrs]; };
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fCCAC = derive2 { name="fCCAC"; version="1.22.0"; sha256="1dn8srjg505725l3arx3cajd2zf0lipq9sqhqrym7km4vlpj58qn"; depends=[ComplexHeatmap fda genomation GenomicRanges ggplot2 IRanges RColorBrewer S4Vectors]; };
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fCI = derive2 { name="fCI"; version="1.26.0"; sha256="17gdknml04m18ds0yjik8h8c778r0jqpd182yhzfzq2gldngnaya"; depends=[FNN gtools psych rgl VennDiagram zoo]; };
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fabia = derive2 { name="fabia"; version="2.42.0"; sha256="04apwymadah5vidbyg0ayp1lx6955c2626zgb6lhj6jhkhzqqxdv"; depends=[Biobase]; };
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factDesign = derive2 { name="factDesign"; version="1.72.0"; sha256="0q6bd3fv6s3br19wivaf2qpcxafw244nvipxixp8ss7a4zgn4qf7"; depends=[Biobase]; };
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famat = derive2 { name="famat"; version="1.5.0"; sha256="03gqkfss1prrchsawyfflzdw6bynjrwk3sxy78xzibh7w0ikkzsh"; depends=[clusterProfiler dplyr DT GO_db gprofiler2 KEGGREST magrittr MPINet ontologyIndex org_Hs_eg_db plotly reactome_db rWikiPathways shiny shinyBS shinydashboard stringr tidyr]; };
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famat = derive2 { name="famat"; version="1.5.0"; sha256="03gqkfss1prrchsawyfflzdw6bynjrwk3sxy78xzibh7w0ikkzsh"; depends=[clusterProfiler dplyr DT GO_db gprofiler2 KEGGREST magrittr ontologyIndex org_Hs_eg_db plotly reactome_db rWikiPathways shiny shinyBS shinydashboard stringr tidyr]; };
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farms = derive2 { name="farms"; version="1.48.0"; sha256="1mnmgd846ayjx1g31pwk186pq6pv0sdq114axpq41728ai3v347c"; depends=[affy Biobase MASS]; };
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fastLiquidAssociation = derive2 { name="fastLiquidAssociation"; version="1.32.0"; sha256="0q6zx6kwgv3lzl2gi8f6c9yzc6vl7kafjfbqnaa7q3a2h26dw9y4"; depends=[doParallel Hmisc impute LiquidAssociation preprocessCore WGCNA]; };
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fastreeR = derive2 { name="fastreeR"; version="1.0.0"; sha256="1skqg527nfpwknyj9k369l4qkzdm02dn262g8v3m4y75i9dw9s58"; depends=[ape data_table dynamicTreeCut R_utils rJava stringr]; };
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@ -1374,7 +1374,7 @@ in with self; {
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flowBeads = derive2 { name="flowBeads"; version="1.34.0"; sha256="1nn19kv3z0pv3hbvazp1x1lmm8rjw392q4d74rsz1hfwz0vj9j97"; depends=[Biobase flowCore knitr rrcov xtable]; };
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flowBin = derive2 { name="flowBin"; version="1.32.0"; sha256="10h7jhadmr1l8qw94fsxcrq581ir9136w91ah84c95m7297nr5r8"; depends=[BiocGenerics class flowCore flowFP limma snow]; };
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flowCHIC = derive2 { name="flowCHIC"; version="1.30.0"; sha256="0zj76ymr6cs27pg0k9gwzr67y5c3iav40fs4rjcjsi26bv5vxpsy"; depends=[EBImage flowCore ggplot2 hexbin vegan]; };
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flowCL = derive2 { name="flowCL"; version="1.34.0"; sha256="05dcxl99sw6d1ngq3wl61y1knmyrf4l9b7nrfmcbigb1isxgjy26"; depends=[graph Rgraphviz SPARQL]; };
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flowCL = derive2 { name="flowCL"; version="1.34.0"; sha256="05dcxl99sw6d1ngq3wl61y1knmyrf4l9b7nrfmcbigb1isxgjy26"; depends=[graph Rgraphviz]; };
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flowClean = derive2 { name="flowClean"; version="1.34.0"; sha256="15kq27136qqplmnj281hi29aakw63r1ip1whj2r87pwhkyz4ifmi"; depends=[bit changepoint flowCore sfsmisc]; };
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flowClust = derive2 { name="flowClust"; version="3.34.0"; sha256="055vm9s8aha92znhpjqkipzprw8bkrinwjaik4ygmhym7w6vbblk"; depends=[Biobase BiocGenerics flowCore graph]; };
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flowCore = derive2 { name="flowCore"; version="2.8.0"; sha256="17nci6rc4i0vs0ibw5q8zy30ap7q4550qpq4ifkbblqbyzxlzkhr"; depends=[BH Biobase BiocGenerics cytolib matrixStats Rcpp RcppArmadillo RProtoBufLib S4Vectors]; };
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@ -1406,7 +1406,7 @@ in with self; {
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frma = derive2 { name="frma"; version="1.48.0"; sha256="1w0q34jkmzqwdjxl4xrvg5nmv11n4l2qf180fwrknvp8am6nf6yx"; depends=[affy Biobase BiocGenerics DBI MASS oligo oligoClasses preprocessCore]; };
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frmaTools = derive2 { name="frmaTools"; version="1.48.0"; sha256="0paas86hfqkvcgv00bbgidcaps8p3gvmfy8prq4rcda4lv8i67bl"; depends=[affy Biobase DBI preprocessCore]; };
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funtooNorm = derive2 { name="funtooNorm"; version="1.20.0"; sha256="02wkjj2nbghwa0ybmh58hl7r2863h9nw95rsd42xzvcp9vxkpfzz"; depends=[GenomeInfoDb IlluminaHumanMethylation450kanno_ilmn12_hg19 IlluminaHumanMethylation450kmanifest matrixStats minfi pls]; };
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gCrisprTools = derive2 { name="gCrisprTools"; version="2.1.5"; sha256="0mi2g46rg4a0sb4774xqbshlj6nj7g0d56pfv35ajkpxdq61g1r1"; depends=[Biobase ComplexHeatmap ggplot2 limma rmarkdown RobustRankAggreg SummarizedExperiment]; };
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gCrisprTools = derive2 { name="gCrisprTools"; version="2.2.1"; sha256="1bq9k3695hxv05f9viw27c73yqmbxhnf60ghk2qv4ixys8lf6fi1"; depends=[Biobase ComplexHeatmap ggplot2 limma rmarkdown SummarizedExperiment]; };
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gaga = derive2 { name="gaga"; version="2.42.0"; sha256="17a2a73lgmgmrkznysd23c1qbddxcsnjdma7xa0pfjwrwskcisxb"; depends=[Biobase coda EBarrays mgcv]; };
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gage = derive2 { name="gage"; version="2.46.0"; sha256="03hx188h98qrbpjlf8v9sg2vqyfv49rp4c18ir11pg6hwqqrxh7b"; depends=[AnnotationDbi GO_db graph KEGGREST]; };
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gaggle = derive2 { name="gaggle"; version="1.64.0"; sha256="1w2819cx7s2hazifhv8iw54jjcvzacjwcpix045ay4fa98ryg7fz"; depends=[graph rJava RUnit]; };
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@ -1440,16 +1440,16 @@ in with self; {
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gespeR = derive2 { name="gespeR"; version="1.28.0"; sha256="0i2r79k77rkw7yhwvpzif1m0llfxv42i9inad7i46630dxpwa1bf"; depends=[Biobase biomaRt cellHTS2 doParallel dplyr foreach ggplot2 glmnet Matrix reshape2]; };
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getDEE2 = derive2 { name="getDEE2"; version="1.6.0"; sha256="0c2air5mra7g80y7r7qpy2hplrh2k38jj5zn4sa5a4fcpniifx7v"; depends=[htm2txt SummarizedExperiment]; };
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geva = derive2 { name="geva"; version="1.4.0"; sha256="0zc9zxw2bifkkiqivmg8bf8xn9sff13bih55k9nxdabsgkkwhyad"; depends=[dbscan fastcluster matrixStats]; };
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ggbio = derive2 { name="ggbio"; version="1.44.0"; sha256="1lvms07ba99nzf10gpn50wjca84nj5jrb6902z069p2bfi4xyd27"; depends=[AnnotationDbi AnnotationFilter Biobase BiocGenerics Biostrings biovizBase BSgenome ensembldb GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges GGally ggplot2 gridExtra gtable Hmisc IRanges OrganismDbi reshape2 rlang Rsamtools rtracklayer S4Vectors scales SummarizedExperiment VariantAnnotation]; };
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ggbio = derive2 { name="ggbio"; version="1.44.1"; sha256="0iyhjalwq1jmldpn20iv8l2kmz6sm20ddry2yz2zn7yq0wszp3vg"; depends=[AnnotationDbi AnnotationFilter Biobase BiocGenerics Biostrings biovizBase BSgenome ensembldb GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges GGally ggplot2 gridExtra gtable Hmisc IRanges OrganismDbi reshape2 rlang Rsamtools rtracklayer S4Vectors scales SummarizedExperiment VariantAnnotation]; };
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ggcyto = derive2 { name="ggcyto"; version="1.24.0"; sha256="0sycyvdpa77mykzr709a7padh6478zmnzapibbq90qkc7bxnj359"; depends=[data_table flowCore flowWorkspace ggplot2 gridExtra hexbin ncdfFlow plyr RColorBrewer rlang scales]; };
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ggmanh = derive2 { name="ggmanh"; version="1.0.0"; sha256="0bcdjvhablnxvakin5a4yhdpv5y5n9rqm21yz51mwjdfgz00p2mb"; depends=[gdsfmt ggplot2 ggrepel RColorBrewer rlang scales SeqArray]; };
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ggmsa = derive2 { name="ggmsa"; version="1.2.0"; sha256="0yrzx780dhs6kgs82gw63i1hxz8nbb9gzw2brc2rl1j1kfp6pp9l"; depends=[aplot Biostrings dplyr ggalt ggforce ggplot2 magrittr R4RNA RColorBrewer seqmagick tidyr]; };
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ggmsa = derive2 { name="ggmsa"; version="1.2.3"; sha256="12s6bs8b8lgcllc540dn4mjdvij2cx28l7zgnz8yzcb05dqnisbr"; depends=[aplot Biostrings dplyr ggalt ggforce ggplot2 ggtree magrittr R4RNA RColorBrewer seqmagick statebins tidyr]; };
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ggspavis = derive2 { name="ggspavis"; version="1.2.0"; sha256="0m0wfswz1jn7zhq527qa7q1x028zzrhg1zkw781w5p5i7ky0qzqf"; depends=[ggplot2 ggside SingleCellExperiment SpatialExperiment SummarizedExperiment]; };
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ggtree = derive2 { name="ggtree"; version="3.4.0"; sha256="033r748npv0l72yb9sk6lqnj0l7cd36ykf788145qv8ck5i2gyk4"; depends=[ape aplot dplyr ggfun ggplot2 magrittr purrr rlang scales tidyr tidytree treeio yulab_utils]; };
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ggtreeExtra = derive2 { name="ggtreeExtra"; version="1.6.0"; sha256="02qbjw8yq9p1qw4gh9dz38iw0qpry8jizp22h2l8wrnkxxg0bllg"; depends=[ggnewscale ggplot2 ggtree rlang tidytree]; };
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girafe = derive2 { name="girafe"; version="1.48.0"; sha256="0633w8dyzrwqgnzj7zhr1hwqh617qpcp7cvs33pgsyxmdh52i32p"; depends=[Biobase BiocGenerics Biostrings genomeIntervals intervals IRanges Rsamtools S4Vectors ShortRead]; };
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glmGamPoi = derive2 { name="glmGamPoi"; version="1.8.0"; sha256="0k1qyljg89jvc4g3ixv8n50a1fmw3yfa7xjdvrfhbk3xsm6n1lh9"; depends=[beachmat BiocGenerics DelayedArray DelayedMatrixStats HDF5Array matrixStats Rcpp RcppArmadillo SummarizedExperiment]; };
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glmSparseNet = derive2 { name="glmSparseNet"; version="1.14.0"; sha256="0yvnmv7360a9fn5zsdnjf02b1xsl6r67gpj25x5vq83cl5gq5ac4"; depends=[biomaRt digest dplyr forcats futile_logger futile_options ggplot2 glmnet glue httr Matrix MultiAssayExperiment readr reshape2 stringr SummarizedExperiment survminer]; };
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glmSparseNet = derive2 { name="glmSparseNet"; version="1.14.1"; sha256="0xpbxgrfrgysnfcj757a0i9235pivwpga5xz052izyw2p5nfrlr2"; depends=[biomaRt digest dplyr forcats futile_logger futile_options ggplot2 glmnet glue httr Matrix MultiAssayExperiment readr reshape2 stringr SummarizedExperiment survminer]; };
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globalSeq = derive2 { name="globalSeq"; version="1.24.0"; sha256="03fb4cd4nbyik7qjblq1fr94gn2xv6jvnb0jzxksdfb7lj8b0axi"; depends=[]; };
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globaltest = derive2 { name="globaltest"; version="5.50.0"; sha256="0mdh9xm9l70i5y4783xv76arx0601w6sz3l8h5bmpsavsz8kc9s5"; depends=[annotate AnnotationDbi Biobase survival]; };
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gmapR = derive2 { name="gmapR"; version="1.38.0"; sha256="0xmc9js5wpnaggf3ldplyxw5w4f2abavlsfzirr2qpik0ha8f7v8"; depends=[Biobase BiocGenerics BiocParallel Biostrings BSgenome GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges Rsamtools rtracklayer S4Vectors VariantAnnotation]; };
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@ -1460,23 +1460,23 @@ in with self; {
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goseq = derive2 { name="goseq"; version="1.48.0"; sha256="1w0rwzhqkvp2x7y5v0qcyjbss0p95gb1jrnx5sdkqginbvrmrd48"; depends=[AnnotationDbi BiasedUrn BiocGenerics geneLenDataBase GO_db mgcv]; };
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gpart = derive2 { name="gpart"; version="1.13.0"; sha256="1518wjkaw22ckgpwl6si83bhijvib0r0kgs9s4das41f0ygi92sd"; depends=[AnnotationDbi biomaRt data_table GenomicRanges Homo_sapiens igraph IRanges OrganismDbi Rcpp TxDb_Hsapiens_UCSC_hg38_knownGene]; };
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gpls = derive2 { name="gpls"; version="1.68.0"; sha256="0ai49lk7pba7k42p9wb67sp744gvkkb2rgfqzdpdwnjmndfxqyib"; depends=[]; };
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gprege = derive2 { name="gprege"; version="1.39.0"; sha256="12yjyb7a7jc86hdi3a3cavqxfzkhmds1m2vigzw5ihhx6028pa78"; depends=[gptk]; };
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gprege = derive2 { name="gprege"; version="1.39.0"; sha256="12yjyb7a7jc86hdi3a3cavqxfzkhmds1m2vigzw5ihhx6028pa78"; depends=[]; };
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gpuMagic = derive2 { name="gpuMagic"; version="1.12.0"; sha256="1g6zxs0wjj6fh23iv65iagyc8lrnzdjkbjv1yf8fq57brzhdl8zl"; depends=[BiocGenerics Deriv DescTools digest pryr Rcpp stringr]; };
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granulator = derive2 { name="granulator"; version="1.4.0"; sha256="0bw07kcrg3cwd73crfgm71hdjrp9pprrg5mzx55rmabymn78915s"; depends=[cowplot dplyr dtangle e1071 epiR ggplot2 ggplotify limSolve magrittr MASS nnls pheatmap purrr rlang tibble tidyr]; };
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graper = derive2 { name="graper"; version="1.12.0"; sha256="18dfk4d9cxgzmgb8wbagd1qlvlpwgs6nzdz6nzif6n4l6jg8x4b7"; depends=[BH cowplot ggplot2 Matrix matrixStats Rcpp RcppArmadillo]; };
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graph = derive2 { name="graph"; version="1.74.0"; sha256="1b8hrjwjg82kicls1496fxfzv75xjvq2k6r9apzsd3qlbyg3ilg4"; depends=[BiocGenerics]; };
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graphite = derive2 { name="graphite"; version="1.42.0"; sha256="0nl5mkgrvf7vsqjy48ij9b1dmxfvp9lf8cpay55h93c4qz4x606g"; depends=[AnnotationDbi graph httr rappdirs rlang]; };
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groHMM = derive2 { name="groHMM"; version="1.29.1"; sha256="03g904s3aydyap94bp69pfv6iwxp0pq7j09210ss6y2pzdk2xilm"; depends=[GenomeInfoDb GenomicAlignments GenomicRanges IRanges MASS rtracklayer S4Vectors]; };
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groHMM = derive2 { name="groHMM"; version="1.30.1"; sha256="0v2mk7xcy483w2nygpmyjp73kj3v5pkk1kf1wr41n33dxqlddqai"; depends=[GenomeInfoDb GenomicAlignments GenomicRanges IRanges MASS rtracklayer S4Vectors]; };
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gscreend = derive2 { name="gscreend"; version="1.10.0"; sha256="1dymj9s11nqjv25a3adnhllkgi5dw5lvhgxkg6sd7qpkh1bvbmrx"; depends=[BiocParallel fGarch nloptr SummarizedExperiment]; };
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gsean = derive2 { name="gsean"; version="1.16.0"; sha256="1vp51nm7bydwljfl9bz4rvqdb5w7yj9zvm74373p2r1pad24r511"; depends=[fgsea PPInfer]; };
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gtrellis = derive2 { name="gtrellis"; version="1.28.0"; sha256="1s4xczzv6hz2kyv32xgcq84540w75qr3f644w1s4c3kwxgyq2gff"; depends=[circlize GenomicRanges GetoptLong IRanges]; };
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gwascat = derive2 { name="gwascat"; version="2.28.0"; sha256="1k4mxpldmvcp0wmyizs5yf45i09ww0lsq159p067490sgngvai8y"; depends=[AnnotationDbi AnnotationHub BiocFileCache Biostrings GenomeInfoDb GenomicFeatures GenomicRanges IRanges readr S4Vectors snpStats VariantAnnotation]; };
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gwascat = derive2 { name="gwascat"; version="2.28.1"; sha256="19ymdxj8966i4yk0zalfw23938cpv4q7pywg4qb242p44na5y9sl"; depends=[AnnotationDbi AnnotationHub BiocFileCache Biostrings GenomeInfoDb GenomicFeatures GenomicRanges IRanges readr S4Vectors snpStats VariantAnnotation]; };
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gwasurvivr = derive2 { name="gwasurvivr"; version="1.14.0"; sha256="1cdknh3ib417ni76wcbns54syqycslj0nzip4pw3sqnsif361ak0"; depends=[GWASTools matrixStats SNPRelate SummarizedExperiment survival VariantAnnotation]; };
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h5vc = derive2 { name="h5vc"; version="2.30.0"; sha256="01vvf4bf4a5sfj5rz1b3bc8smvw3j260q4q11bqbq2xaw5lg64q7"; depends=[abind BatchJobs BiocParallel Biostrings GenomeInfoDb GenomicRanges ggplot2 gridExtra h5vcData IRanges reshape rhdf5 Rhtslib Rsamtools S4Vectors]; };
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hapFabia = derive2 { name="hapFabia"; version="1.38.0"; sha256="1l50p1hnym8amvdfazp36zp3ijbfsgd8sddbcqivd3rp01898mmr"; depends=[Biobase fabia]; };
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hca = derive2 { name="hca"; version="1.4.0"; sha256="0i2q4vqz95vncxvd4wgsyza24k5rgjilxlpgs90r9ilzfnvs13h0"; depends=[BiocFileCache digest dplyr httr jsonlite readr tibble tidyr]; };
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heatmaps = derive2 { name="heatmaps"; version="1.20.0"; sha256="137cblqfn3w2nrlkffrxhpv1fd0ygy8njqf3n09gf2qw4vgzyz0g"; depends=[BiocGenerics Biostrings EBImage GenomeInfoDb GenomicRanges IRanges KernSmooth Matrix plotrix RColorBrewer]; };
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hermes = derive2 { name="hermes"; version="0.99.4"; sha256="0vf7gkfn1108hpq3asgdv8n34wgwxpgjz9wfawfhr4zldklfgg6f"; depends=[assertthat Biobase BiocGenerics biomaRt checkmate circlize ComplexHeatmap DESeq2 dplyr edgeR EnvStats forcats GenomicRanges ggfortify ggplot2 ggrepel IRanges lifecycle limma magrittr matrixStats MultiAssayExperiment purrr R6 Rdpack rlang S4Vectors SummarizedExperiment tidyr]; };
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hermes = derive2 { name="hermes"; version="1.0.1"; sha256="0l4rynsz03s4rrdf6pn7sq6x9ra11lal9w65fwxvg1qk83b1gcx4"; depends=[assertthat Biobase BiocGenerics biomaRt checkmate circlize ComplexHeatmap DESeq2 dplyr edgeR EnvStats forcats GenomicRanges ggfortify ggplot2 ggrepel IRanges lifecycle limma magrittr matrixStats MultiAssayExperiment purrr R6 Rdpack rlang S4Vectors SummarizedExperiment tidyr]; };
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hiAnnotator = derive2 { name="hiAnnotator"; version="1.30.0"; sha256="0f1imlql09dgckcvf3dr7knr26yjs0r1ryrq54r1lwz57s3rn152"; depends=[BSgenome dplyr foreach GenomicRanges ggplot2 iterators rtracklayer scales]; };
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hiReadsProcessor = derive2 { name="hiReadsProcessor"; version="1.32.0"; sha256="0cf0ris5c2xbbmsjnww9lwmmlhya21gmhxfsmcid4bi9gs94qpci"; depends=[BiocGenerics BiocParallel Biostrings dplyr GenomicAlignments GenomicRanges hiAnnotator readxl sonicLength]; };
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hierGWAS = derive2 { name="hierGWAS"; version="1.26.0"; sha256="0n8rbk3whs6ysjkdz6zwvdbw5gqrriyzdmyz2b09h6w1dl61cy43"; depends=[fastcluster fmsb glmnet]; };
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@ -1514,7 +1514,7 @@ in with self; {
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igvR = derive2 { name="igvR"; version="1.16.0"; sha256="0jaj600dcis1xd4hp6zw3j92zqi476zxlnb3lhcsszx7rg6lqnfp"; depends=[BiocGenerics BrowserViz GenomicAlignments GenomicRanges httpuv MotifDb RColorBrewer rtracklayer seqLogo VariantAnnotation]; };
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illuminaio = derive2 { name="illuminaio"; version="0.38.0"; sha256="1xk057a9w4ps8xi8jyw8imkjcicfmzns8g92grn4af7yiip68h62"; depends=[base64]; };
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imageHTS = derive2 { name="imageHTS"; version="1.45.1"; sha256="18cv1mss1vgm4zwx37nijc1riw2n9lwl73l2cfiqglblgdmyq2sm"; depends=[Biobase cellHTS2 e1071 EBImage hwriter vsn]; };
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imcRtools = derive2 { name="imcRtools"; version="1.2.1"; sha256="1mkdi35amb0jlgk4kmbgfvwn1p1sss45zahhra8anrs1qzn6x2gm"; depends=[abind BiocNeighbors BiocParallel concaveman cytomapper data_table dplyr DT EBImage ggplot2 ggraph igraph magrittr pheatmap readr RTriangle S4Vectors scuttle sf SingleCellExperiment SpatialExperiment stringr SummarizedExperiment tidygraph viridis vroom]; };
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imcRtools = derive2 { name="imcRtools"; version="1.2.3"; sha256="1a2gapm9642x7a4m9cl95fpl6qq3zrhgvib8rqzx465d0p47szfw"; depends=[abind BiocNeighbors BiocParallel concaveman cytomapper data_table dplyr DT EBImage ggplot2 ggraph igraph magrittr pheatmap readr RTriangle S4Vectors scuttle sf SingleCellExperiment SpatialExperiment stringr SummarizedExperiment tidygraph viridis vroom]; };
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immunoClust = derive2 { name="immunoClust"; version="1.28.0"; sha256="10dwlg91wg38s97hivd8fm4wkmv0nv7xcw8dwdh2g7m5pip7nchp"; depends=[flowCore lattice]; };
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immunotation = derive2 { name="immunotation"; version="1.4.0"; sha256="06yknvqz65x3vgc9xykdwhsgqhz75jr038fwnjjr2ir8x9h6fri5"; depends=[curl ggplot2 maps ontologyIndex readr rlang rvest stringr tidyr xml2]; };
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impute = derive2 { name="impute"; version="1.70.0"; sha256="11b0z7py0im6y43k55xpzz5jnvc0ram9rk3n1n4mwhvs0vhy39r2"; depends=[]; };
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@ -1527,7 +1527,7 @@ in with self; {
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inveRsion = derive2 { name="inveRsion"; version="1.43.0"; sha256="0h2q10xf4x22hy7780w4pvq488921wzjngly8qcc97sa8iacssk3"; depends=[haplo_stats]; };
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ipdDb = derive2 { name="ipdDb"; version="1.14.0"; sha256="12wnl8gpkwvp3lvdw5qfjy8n2wpwgm7hgp0cx4lysyr7hchfjzi1"; depends=[AnnotationDbi AnnotationHub assertthat Biostrings DBI GenomicRanges IRanges RSQLite]; };
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isobar = derive2 { name="isobar"; version="1.42.0"; sha256="1z8qxdd4kqdi55g84lb8268nd270y4knzrpcm3b1gvxd91pynbq4"; depends=[Biobase biomaRt distr ggplot2 plyr]; };
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isomiRs = derive2 { name="isomiRs"; version="1.24.0"; sha256="1w7fqfs8ncml52cy2g8i7phf2j2g1pw3wbsxhrkjipzzq6vk0h41"; depends=[AnnotationDbi assertive_sets Biobase BiocGenerics broom cluster cowplot DEGreport DESeq2 DiscriMiner dplyr GenomicRanges GGally ggplot2 gplots gridExtra gtools IRanges limma RColorBrewer readr reshape rlang S4Vectors stringr SummarizedExperiment tibble tidyr]; };
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isomiRs = derive2 { name="isomiRs"; version="1.24.0"; sha256="1w7fqfs8ncml52cy2g8i7phf2j2g1pw3wbsxhrkjipzzq6vk0h41"; depends=[AnnotationDbi assertive_sets Biobase BiocGenerics broom cluster cowplot DEGreport DESeq2 dplyr GenomicRanges GGally ggplot2 gplots gridExtra gtools IRanges limma RColorBrewer readr reshape rlang S4Vectors stringr SummarizedExperiment tibble tidyr]; };
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iterClust = derive2 { name="iterClust"; version="1.18.0"; sha256="11j6ssy88v0wxqkx9b4skqi8jww8b4nh1gjl8smlnw98lvf5vwl4"; depends=[Biobase cluster]; };
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iterativeBMA = derive2 { name="iterativeBMA"; version="1.54.0"; sha256="1ykn4cac33w85gxh1bbqcg06xx0jsx1ivq4477h0057y3vf09cck"; depends=[Biobase BMA leaps]; };
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iterativeBMAsurv = derive2 { name="iterativeBMAsurv"; version="1.54.0"; sha256="0fll6aqmh4dbrn4pv8nwp5cnsc2jd40clfnb76zzgi6qka5h2kms"; depends=[BMA leaps survival]; };
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@ -1543,7 +1543,7 @@ in with self; {
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les = derive2 { name="les"; version="1.46.0"; sha256="07c805gcyc7b462hbkvkkjajk8sn735j1js452lz67ixf03pwcaq"; depends=[boot fdrtool gplots RColorBrewer]; };
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levi = derive2 { name="levi"; version="1.14.0"; sha256="1dh314yd0zpnmi2vfnf41fhzpg76cgwgzkbm93vcxwrszj53cljc"; depends=[colorspace dplyr DT ggplot2 httr igraph knitr RColorBrewer Rcpp reshape2 rmarkdown shiny shinydashboard shinyjs testthat xml2]; };
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lfa = derive2 { name="lfa"; version="1.26.0"; sha256="044866h4fnxmzb3sh9vmrd2smgsbcqgvd19dgwxisi418cad577l"; depends=[corpcor]; };
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limma = derive2 { name="limma"; version="3.52.0"; sha256="1hzxcsbpm1qrbz2fwq4s3v6xcnvbdzzkhk5chp7w3i1qqkccks1l"; depends=[]; };
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limma = derive2 { name="limma"; version="3.52.2"; sha256="0m8p8pqmf48f2zdf3qs66hmychbc58g2hfg1wyxzsv180m6xkk65"; depends=[]; };
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limmaGUI = derive2 { name="limmaGUI"; version="1.72.0"; sha256="1sq20bdnc9j93iink9cs1p50alzgqfjcxikr8p0dfvd96c4js5b7"; depends=[limma R2HTML tkrplot xtable]; };
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lineagespot = derive2 { name="lineagespot"; version="1.0.0"; sha256="0bn0rr7c8x576p53d7p7q0hs7dh5y7dm4z5dgcrp9m8pqgdq3n9h"; depends=[data_table httr MatrixGenerics stringr SummarizedExperiment VariantAnnotation]; };
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lionessR = derive2 { name="lionessR"; version="1.10.0"; sha256="182hyz7acnlmprfn3555d1li73abahkylznrnqzizyi20r3nwczq"; depends=[S4Vectors SummarizedExperiment]; };
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@ -1583,7 +1583,7 @@ in with self; {
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mdp = derive2 { name="mdp"; version="1.16.0"; sha256="1r7w7mzq6a31rjfnpbanvvk95nai189bggw4kj8y08k8kf44hsji"; depends=[ggplot2 gridExtra]; };
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mdqc = derive2 { name="mdqc"; version="1.58.0"; sha256="132spf0yhc864f8adsavyljcnmq28p1cpw8clb0rsi1v3hrj6kn5"; depends=[cluster MASS]; };
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megadepth = derive2 { name="megadepth"; version="1.6.0"; sha256="0qq82dmd3drr2bhn51bgbc6ml40klfmmhj6wdj72n9ya6n60lwy8"; depends=[cmdfun dplyr fs GenomicRanges magrittr readr xfun]; };
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memes = derive2 { name="memes"; version="1.4.0"; sha256="02069p4izgxjwjcjjd7bd8x92sfishdrff8b0xyv1p631cxcbk5c"; depends=[Biostrings cmdfun dplyr GenomicRanges ggplot2 ggseqlogo magrittr matrixStats patchwork processx purrr readr rlang tibble tidyr universalmotif usethis xml2]; };
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memes = derive2 { name="memes"; version="1.4.1"; sha256="1s0mdfhvq52vg3494wgh4ar8vax5bc99gqsaism3d7vi4h9wnhzn"; depends=[Biostrings cmdfun dplyr GenomicRanges ggplot2 ggseqlogo magrittr matrixStats patchwork processx purrr readr rlang tibble tidyr universalmotif usethis xml2]; };
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meshes = derive2 { name="meshes"; version="1.22.0"; sha256="1affs7w2rwzkl2gh895ixwpvmp158acx1i4vcjg25gvak3wnwapq"; depends=[AnnotationDbi AnnotationHub DOSE enrichplot GOSemSim MeSHDbi yulab_utils]; };
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meshr = derive2 { name="meshr"; version="2.2.0"; sha256="1gaxjz5day6xipfh8dy0nxf7vxnvdy9b9hfdp83ysyhxszb36fdl"; depends=[BiocGenerics BiocStyle Category fdrtool knitr markdown MeSHDbi rmarkdown RSQLite S4Vectors]; };
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messina = derive2 { name="messina"; version="1.32.0"; sha256="1avfj9xdx1mi7f1sdl9j1xf1jhj5cibkiwwy7aa1w7chz1mz8hr4"; depends=[foreach ggplot2 plyr Rcpp survival]; };
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@ -1593,7 +1593,7 @@ in with self; {
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metabCombiner = derive2 { name="metabCombiner"; version="1.6.0"; sha256="1vnh0bqfzknpflk0j5y9jxggmc3m4irxyfbkm9jf6k5a30fnmmxb"; depends=[caret dplyr matrixStats mgcv rlang S4Vectors tidyr]; };
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metabolomicsWorkbenchR = derive2 { name="metabolomicsWorkbenchR"; version="1.6.0"; sha256="0mg7wrg8qgv11w7179nrw5w7209qjqbirm9niz2ygw1pidg0slc8"; depends=[data_table httr jsonlite MultiAssayExperiment struct SummarizedExperiment]; };
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metabomxtr = derive2 { name="metabomxtr"; version="1.30.0"; sha256="0z02b91gd71b5ksfk2ql5jldicsqh66z2yvv5yyws98xl0qqrrxw"; depends=[Biobase BiocParallel Formula ggplot2 multtest optimx plyr]; };
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metagene = derive2 { name="metagene"; version="2.28.0"; sha256="131ymnrwj1ywdf78yd3fffsl6yis9dsizvjhddkqssavz2d4xy71"; depends=[BiocParallel data_table EnsDb_Hsapiens_v86 ensembldb GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 gplots IRanges magrittr matrixStats muStat purrr R6 Rsamtools rtracklayer stringr]; };
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metagene = derive2 { name="metagene"; version="2.28.0"; sha256="131ymnrwj1ywdf78yd3fffsl6yis9dsizvjhddkqssavz2d4xy71"; depends=[BiocParallel data_table EnsDb_Hsapiens_v86 ensembldb GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 gplots IRanges magrittr matrixStats purrr R6 Rsamtools rtracklayer stringr]; };
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metagene2 = derive2 { name="metagene2"; version="1.12.0"; sha256="1606i1kw8i4q1m07x2yax2mfmj9knzd7jiqgzq3fn792z1yj1bsb"; depends=[BiocParallel data_table dplyr GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 IRanges magrittr purrr R6 reshape2 Rsamtools rtracklayer]; };
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metagenomeSeq = derive2 { name="metagenomeSeq"; version="1.38.0"; sha256="0v8h8ld4gzq0v90hfprw3v8j2hlac44wxyj2m6qmz0y5hml97k02"; depends=[Biobase foreach glmnet gplots limma Matrix matrixStats RColorBrewer Wrench]; };
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metahdep = derive2 { name="metahdep"; version="1.54.0"; sha256="1y8pr873jy1ax8n8qp8kihagddk5j03pjwmxff03amnqrnxyphlv"; depends=[]; };
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@ -1605,7 +1605,7 @@ in with self; {
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methimpute = derive2 { name="methimpute"; version="1.18.0"; sha256="1d197yf3hfnag6s2pr7vy69vmrh1v8bdxwfylb7v7xsjkhjb1nv7"; depends=[Biostrings data_table GenomeInfoDb GenomicRanges ggplot2 IRanges minpack_lm Rcpp reshape2]; };
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methrix = derive2 { name="methrix"; version="1.10.0"; sha256="0717pazv7yakj3b0c8p7rzb4iykyiv8vh02c4357qc3kwarkpncj"; depends=[BSgenome data_table DelayedArray DelayedMatrixStats GenomicRanges ggplot2 HDF5Array IRanges matrixStats rtracklayer SummarizedExperiment]; };
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methylCC = derive2 { name="methylCC"; version="1.10.0"; sha256="0sigx62cy47cmpirr6nqcdik5dxkn79j2xjap36jmipaa2i914s2"; depends=[Biobase bsseq bumphunter dplyr FlowSorted_Blood_450k genefilter GenomicRanges IlluminaHumanMethylation450kanno_ilmn12_hg19 IlluminaHumanMethylation450kmanifest IRanges magrittr minfi plyranges quadprog S4Vectors]; };
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methylGSA = derive2 { name="methylGSA"; version="1.14.0"; sha256="0lmzipk9mn3m0nv9fmfc5q53w7f1pz37cyj18n501p3p6ljqhz3r"; depends=[AnnotationDbi BiocParallel clusterProfiler ggplot2 GO_db IlluminaHumanMethylation450kanno_ilmn12_hg19 IlluminaHumanMethylationEPICanno_ilm10b4_hg19 missMethyl org_Hs_eg_db reactome_db RobustRankAggreg shiny stringr]; };
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methylGSA = derive2 { name="methylGSA"; version="1.14.0"; sha256="0lmzipk9mn3m0nv9fmfc5q53w7f1pz37cyj18n501p3p6ljqhz3r"; depends=[AnnotationDbi BiocParallel clusterProfiler ggplot2 GO_db IlluminaHumanMethylation450kanno_ilmn12_hg19 IlluminaHumanMethylationEPICanno_ilm10b4_hg19 missMethyl org_Hs_eg_db reactome_db shiny stringr]; };
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methylInheritance = derive2 { name="methylInheritance"; version="1.20.0"; sha256="0a0rgi396jghxpsq44ybn518r8qkz329kpnpfb0jggwc8ygg56id"; depends=[BiocParallel GenomicRanges ggplot2 gridExtra IRanges methylKit rebus S4Vectors]; };
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methylKit = derive2 { name="methylKit"; version="1.22.0"; sha256="00asjzv05avfg0rrkmfbdqd6xx8d18zi72n3b1kf9wj81z2d2a35"; depends=[data_table emdbook fastseg GenomeInfoDb GenomicRanges gtools IRanges KernSmooth limma mclust mgcv qvalue R_utils Rcpp Rhtslib Rsamtools rtracklayer S4Vectors zlibbioc]; };
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methylMnM = derive2 { name="methylMnM"; version="1.34.0"; sha256="1mxkxs06j8mi44rqnzz52dnarhh1x120qqxwkdlggl8ll36zkhrm"; depends=[edgeR statmod]; };
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@ -1633,7 +1633,7 @@ in with self; {
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microbiome = derive2 { name="microbiome"; version="1.18.0"; sha256="1z9arkjp5xszlg07mzb4p163i74jfbd9p4gbwv5syivnpl040k12"; depends=[Biostrings compositions dplyr ggplot2 phyloseq reshape2 Rtsne scales tibble tidyr vegan]; };
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microbiomeDASim = derive2 { name="microbiomeDASim"; version="1.10.0"; sha256="05lj8ihx8cpx2casxbpyn7n3zwia0bmj0lyn9prqial56s0zmsaj"; depends=[Biobase ggplot2 MASS Matrix metagenomeSeq mvtnorm pbapply phyloseq tmvtnorm]; };
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microbiomeExplorer = derive2 { name="microbiomeExplorer"; version="1.6.0"; sha256="0h4flm07n56biviramydxjzcrzxq5n0rr1295mjsxngnpg83kvp8"; depends=[Biobase biomformat broom car DESeq2 dplyr DT forcats heatmaply knitr limma lubridate magrittr matrixStats metagenomeSeq plotly purrr RColorBrewer readr reshape2 rlang rmarkdown shiny shinycssloaders shinydashboard shinyjs shinyWidgets stringr tibble tidyr vegan]; };
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microbiomeMarker = derive2 { name="microbiomeMarker"; version="1.2.0"; sha256="0ldhwfpqkyn8qhnv1y8757cwiq7z6vggf1zxxj453s3i4qpbj4lb"; depends=[ALDEx2 ANCOMBC Biobase BiocGenerics biomformat Biostrings caret coin ComplexHeatmap DESeq2 dplyr edgeR ggplot2 ggsignif ggtree IRanges limma magrittr MASS metagenomeSeq multtest patchwork phyloseq plotROC purrr rlang S4Vectors tibble tidyr tidytree yaml]; };
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microbiomeMarker = derive2 { name="microbiomeMarker"; version="1.2.2"; sha256="0bd5a92na9hk2hpmqphpdhn24pk1p2gk5nsbslp8yk5c4161qxmk"; depends=[ALDEx2 ANCOMBC Biobase BiocGenerics BiocParallel biomformat Biostrings caret coin ComplexHeatmap DESeq2 dplyr edgeR ggplot2 ggsignif ggtree IRanges limma magrittr MASS metagenomeSeq multtest patchwork phyloseq plotROC pROC purrr rlang S4Vectors tibble tidyr tidytree vegan yaml]; };
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midasHLA = derive2 { name="midasHLA"; version="1.4.0"; sha256="1xvqrsp6rkcnr8fnjr9g62krwwshiy3xapxlmbi4bhm6605b0ccy"; depends=[assertthat broom dplyr formattable HardyWeinberg kableExtra knitr magrittr MultiAssayExperiment qdapTools rlang S4Vectors stringi SummarizedExperiment tibble]; };
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miloR = derive2 { name="miloR"; version="1.4.0"; sha256="1jz9p3grnczx0bpdw6j64x21in8zgm3qy19hmm296har2rx9m5zs"; depends=[BiocGenerics BiocNeighbors BiocParallel BiocSingular cowplot dplyr edgeR ggbeeswarm ggplot2 ggraph ggrepel gtools igraph irlba limma Matrix matrixStats patchwork RColorBrewer S4Vectors SingleCellExperiment stringr SummarizedExperiment tibble tidyr]; };
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mimager = derive2 { name="mimager"; version="1.20.0"; sha256="1iy1bghz3wqn80444h9aq81mz1pw7wcx0m6bjj33qxdzcr66jbgl"; depends=[affy affyPLM Biobase BiocGenerics DBI gtable oligo oligoClasses preprocessCore S4Vectors scales]; };
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@ -1652,7 +1652,7 @@ in with self; {
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moanin = derive2 { name="moanin"; version="1.4.0"; sha256="0k3k554ncm4j3zkz67dlzdvii9m6k117gryj7lk9wrbsv1a0y7if"; depends=[ClusterR edgeR limma MASS matrixStats NMI reshape2 S4Vectors SummarizedExperiment topGO viridis zoo]; };
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mogsa = derive2 { name="mogsa"; version="1.30.0"; sha256="1yxnkwf6f356nm999b2ng54zb4cdi94pxhpwzj3f3rnr31jawvlp"; depends=[Biobase BiocGenerics cluster corpcor genefilter gplots graphite GSEABase svd]; };
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monaLisa = derive2 { name="monaLisa"; version="1.2.0"; sha256="0rqqkry54cz7id87znc59d8x49z8cwckmx30nxr6razmyl5bqmx6"; depends=[BiocGenerics BiocParallel Biostrings BSgenome circlize ComplexHeatmap GenomeInfoDb GenomicRanges glmnet IRanges S4Vectors stabs SummarizedExperiment TFBSTools vioplot XVector]; };
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monocle = derive2 { name="monocle"; version="2.24.0"; sha256="1fyqd7qhij2iyx9vdmgnx2qf0w3kwbkmg805539zrmxry8cwfldb"; depends=[Biobase BiocGenerics biocViews cluster combinat DDRTree dplyr fastICA ggplot2 HSMMSingleCell igraph irlba leidenbase limma MASS Matrix matrixStats pheatmap plyr proxy qlcMatrix RANN Rcpp reshape2 Rtsne slam stringr tibble VGAM viridis]; };
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monocle = derive2 { name="monocle"; version="2.24.1"; sha256="11g1wx0f1yzhg3x1aa3d5l7pqlzxj16s0gha21skxkgld8k2x8xn"; depends=[Biobase BiocGenerics biocViews cluster combinat DDRTree dplyr fastICA ggplot2 HSMMSingleCell igraph irlba leidenbase limma MASS Matrix matrixStats pheatmap plyr proxy qlcMatrix RANN Rcpp reshape2 Rtsne slam stringr tibble VGAM viridis]; };
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mosaics = derive2 { name="mosaics"; version="2.34.0"; sha256="196wz422a284akariq5iicknaqqcm50v63b57gsi2pzmv6qfmf5y"; depends=[GenomeInfoDb GenomicAlignments GenomicRanges IRanges lattice MASS Rcpp Rsamtools S4Vectors]; };
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mosbi = derive2 { name="mosbi"; version="1.2.0"; sha256="00l9kykr9n8ys3riw4pjqsdskf8klv9j62v0nr66z66646c1a7vp"; depends=[akmbiclust BH biclust fabia igraph isa2 QUBIC RColorBrewer Rcpp RcppParallel xml2]; };
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motifStack = derive2 { name="motifStack"; version="1.40.0"; sha256="0d2ihx73chczbv6f91n04qb372plrdv7k4qws8shyw1fmvb1rq0z"; depends=[ade4 Biostrings ggplot2 htmlwidgets TFBSTools XML]; };
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@ -1677,7 +1677,7 @@ in with self; {
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multiscan = derive2 { name="multiscan"; version="1.56.0"; sha256="0wxpm0np4721nw2gz4db4a1wdi06pnnziyj0mwkwpsll7mgz337p"; depends=[Biobase]; };
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multtest = derive2 { name="multtest"; version="2.52.0"; sha256="037wcmwk1wvhjxgmlvnk289pkwishi1753ajkmy9x14xlmldix82"; depends=[Biobase BiocGenerics MASS survival]; };
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mumosa = derive2 { name="mumosa"; version="1.4.0"; sha256="1zrbajjfjq8mp6qq10xfrq2m2yrnda37s2aba32dwdk1gpkxx9g4"; depends=[batchelor beachmat BiocGenerics BiocNeighbors BiocParallel BiocSingular DelayedArray DelayedMatrixStats igraph IRanges Matrix metapod S4Vectors ScaledMatrix scran scuttle SingleCellExperiment SummarizedExperiment uwot]; };
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muscat = derive2 { name="muscat"; version="1.10.0"; sha256="068kzhggzihvhg3n3sdid4ha4k40rfr9bclxw2qkp69yi8jwqrxr"; depends=[BiocParallel blme ComplexHeatmap data_table DESeq2 dplyr edgeR ggplot2 glmmTMB limma lme4 lmerTest Matrix matrixStats progress purrr S4Vectors scales scater sctransform scuttle SingleCellExperiment SummarizedExperiment variancePartition viridis]; };
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muscat = derive2 { name="muscat"; version="1.10.1"; sha256="1j3zkhqgza92vdykb1yia1jjwsdqra6q9c0jk6p5p2x0778xqgfd"; depends=[BiocParallel blme ComplexHeatmap data_table DESeq2 dplyr edgeR ggplot2 glmmTMB limma lme4 lmerTest Matrix matrixStats progress purrr S4Vectors scales scater sctransform scuttle SingleCellExperiment SummarizedExperiment variancePartition viridis]; };
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muscle = derive2 { name="muscle"; version="3.38.0"; sha256="16qfnf02lmfk1cwwql5airkpv7c90lvpyjjrwicid55gqhajfzhx"; depends=[Biostrings]; };
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musicatk = derive2 { name="musicatk"; version="1.6.0"; sha256="1j3402ywcma83zxbhwlazr0s57c8b11xzg41qfxc6k2dngv3h06z"; depends=[Biostrings BSgenome BSgenome_Hsapiens_UCSC_hg19 BSgenome_Hsapiens_UCSC_hg38 BSgenome_Mmusculus_UCSC_mm10 BSgenome_Mmusculus_UCSC_mm9 cluster ComplexHeatmap cowplot data_table decompTumor2Sig deconstructSigs dplyr factoextra GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 ggrepel gridExtra gtools IRanges maftools magrittr MASS matrixTests MCMCprecision NMF philentropy plotly rlang S4Vectors shiny shinyalert shinyBS shinybusy shinydashboard shinyjqui shinyjs sortable stringi stringr SummarizedExperiment TCGAbiolinks tibble tidyr topicmodels TxDb_Hsapiens_UCSC_hg19_knownGene TxDb_Hsapiens_UCSC_hg38_knownGene uwot VariantAnnotation withr]; };
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mygene = derive2 { name="mygene"; version="1.32.0"; sha256="0j1cwz95hx2wl6mf6kycrw0xlsi4j6s7y4jjm87dq52dnwnh8svy"; depends=[GenomicFeatures Hmisc httr jsonlite plyr S4Vectors sqldf]; };
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@ -1696,15 +1696,15 @@ in with self; {
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netSmooth = derive2 { name="netSmooth"; version="1.16.0"; sha256="0jzid8svq21i5kbc3c908dqmf0i4mlsnfa4bq7avp9ynv195nc4q"; depends=[cluster clusterExperiment data_table DelayedArray entropy HDF5Array Matrix scater SingleCellExperiment SummarizedExperiment]; };
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netZooR = derive2 { name="netZooR"; version="1.0.0"; sha256="03a1i508hm8i86nnlj1i4hz83fz1krp3qfbiyv2yhrdq3f5ra1yr"; depends=[AnnotationDbi assertthat Biobase data_table doParallel dplyr foreach ggdendro ggplot2 GO_db GOstats gplots igraph MASS Matrix matrixStats nnet org_Hs_eg_db pandaR penalized RCy3 reshape reshape2 reticulate STRINGdb tidyr vegan viridisLite yarn]; };
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netbiov = derive2 { name="netbiov"; version="1.30.0"; sha256="1c63ywyp7zcszrrkyx3q4xnkzij17km675825gcmfgk3h0g96lx7"; depends=[igraph]; };
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netboost = derive2 { name="netboost"; version="2.4.0"; sha256="07fk9hpjx8ghfjs5swcd3dckghk0slbbiawhwrk4zw10ysvjnqnm"; depends=[colorspace dynamicTreeCut impute R_utils Rcpp RcppParallel WGCNA]; };
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netboost = derive2 { name="netboost"; version="2.4.1"; sha256="11rayvp15ysk2fkpsw3w3ivkxfk8dznz6zdrnbmfhv1814mbfvk7"; depends=[colorspace dynamicTreeCut impute R_utils Rcpp RcppParallel WGCNA]; };
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netboxr = derive2 { name="netboxr"; version="1.7.1"; sha256="06pc0qw275r1ksj07hvkfvcvxl9dg539wja07j7lbqvnp6hzl0xd"; depends=[clusterProfiler data_table DT gplots igraph jsonlite plyr RColorBrewer]; };
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nethet = derive2 { name="nethet"; version="1.28.0"; sha256="1c6is3w1saw5i2akmxf6272qlbxpf40ayfh19jialmmqsdhik01z"; depends=[CompQuadForm GeneNet ggm ggplot2 glasso glmnet GSA huge ICSNP limma mclust multtest mvtnorm network]; };
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netprioR = derive2 { name="netprioR"; version="1.22.0"; sha256="0wbhcr0qkcsnakfpx49hkjhwbmrc9n76rbs75pc3da4z9wv89qg3"; depends=[doParallel dplyr foreach ggplot2 gridExtra Matrix pROC sparseMVN]; };
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netresponse = derive2 { name="netresponse"; version="1.56.0"; sha256="0ciw89zvahyirjnpc69rdipxzlil6fjd5qmk61fdmr1scvvpv2iv"; depends=[BiocStyle dmt ggplot2 graph igraph mclust minet plyr qvalue RColorBrewer reshape2 Rgraphviz rmarkdown]; };
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netresponse = derive2 { name="netresponse"; version="1.56.0"; sha256="0ciw89zvahyirjnpc69rdipxzlil6fjd5qmk61fdmr1scvvpv2iv"; depends=[BiocStyle ggplot2 graph igraph mclust minet plyr qvalue RColorBrewer reshape2 Rgraphviz rmarkdown]; };
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networkBMA = derive2 { name="networkBMA"; version="2.35.0"; sha256="0xa0b977apbr6p9kqk38582af635kp99csj32bsn2bf8pjsmd4d2"; depends=[BH BMA leaps Rcpp RcppArmadillo RcppEigen]; };
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ngsReports = derive2 { name="ngsReports"; version="1.12.0"; sha256="0xcx1wrdzg4ya42cr8nhgpjkx5d88nqlpjnj6x020v3l0amcqyyh"; depends=[BiocGenerics Biostrings checkmate dplyr DT forcats ggdendro ggplot2 lifecycle lubridate pander plotly readr reshape2 rmarkdown scales stringr tibble tidyr tidyselect zoo]; };
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nnNorm = derive2 { name="nnNorm"; version="2.60.0"; sha256="09xr73xpfzj0w9wx23bqzkcnxlvgc50lazbfpd5phl0ravsl5spl"; depends=[marray nnet]; };
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nnSVG = derive2 { name="nnSVG"; version="1.0.0"; sha256="1sgza1pb3sbz68br0y958qgvdxm684r1ickv9q6fgz8bdp6hdhz1"; depends=[BiocParallel BRISC Matrix matrixStats SingleCellExperiment SpatialExperiment SummarizedExperiment]; };
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nnSVG = derive2 { name="nnSVG"; version="1.0.1"; sha256="092zzf7gkc2k473n1gvayrddvhp1lx1zk58rkmiyfspgbgjky042"; depends=[BiocParallel BRISC Matrix matrixStats SingleCellExperiment SpatialExperiment SummarizedExperiment]; };
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nondetects = derive2 { name="nondetects"; version="2.26.0"; sha256="1y31pzsihqmlhprdgl9xwspbfj2k9zgp15d905v6y9zjzjdxfdhf"; depends=[arm Biobase HTqPCR limma mvtnorm]; };
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normalize450K = derive2 { name="normalize450K"; version="1.24.0"; sha256="03cmxljvcfmzkvsrzhc4si17g68fcb8877pzf6960cvbhv00d4ys"; depends=[Biobase illuminaio quadprog]; };
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normr = derive2 { name="normr"; version="1.22.0"; sha256="1v1x54k8kphq3xrnv5m2ya4viyg22msgviv6hg6qg8fb4hqp9ich"; depends=[bamsignals GenomeInfoDb GenomicRanges IRanges qvalue Rcpp rtracklayer]; };
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@ -1721,7 +1721,7 @@ in with self; {
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omicade4 = derive2 { name="omicade4"; version="1.36.0"; sha256="1l7w3sczsimg640klq8navgdcwjj090wjqd40n4mw76pny2xj2lj"; depends=[ade4 Biobase made4]; };
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omicplotR = derive2 { name="omicplotR"; version="1.16.0"; sha256="0sqh8nympgrig01x4j302xsya10sbrpn75sjwy16srxxiagkrlzk"; depends=[ALDEx2 compositions DT jsonlite knitr matrixStats rmarkdown shiny vegan zCompositions]; };
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omicsPrint = derive2 { name="omicsPrint"; version="1.16.0"; sha256="08gv2qzv7a1jsyqqm802w3awymnnyyy84ic56wzhcdimhqgs0an3"; depends=[MASS matrixStats MultiAssayExperiment RaggedExperiment SummarizedExperiment]; };
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omicsViewer = derive2 { name="omicsViewer"; version="1.0.0"; sha256="1631hqj6r0ar7ymrlb4phsnw9d3x4q20p4702qlfyw6a67drib86"; depends=[beeswarm Biobase curl DT fastmatch fgsea flatxml ggplot2 ggseqlogo htmlwidgets httr Matrix matrixStats networkD3 openxlsx plotly psych RColorBrewer reshape2 RSQLite S4Vectors shiny shinybusy shinycssloaders shinyjs shinythemes shinyWidgets stringr SummarizedExperiment survival survminer]; };
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omicsViewer = derive2 { name="omicsViewer"; version="1.0.1"; sha256="1dndhjwi7n0syp6dq84008df12f628pr0h880qvgfgzfy63g0vnz"; depends=[beeswarm Biobase curl DT fastmatch fgsea flatxml ggplot2 ggseqlogo htmlwidgets httr Matrix matrixStats networkD3 openxlsx plotly psych RColorBrewer reshape2 RSQLite S4Vectors shiny shinybusy shinycssloaders shinyjs shinythemes shinyWidgets stringr SummarizedExperiment survival survminer]; };
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ompBAM = derive2 { name="ompBAM"; version="1.0.0"; sha256="0pjkp6vhnnbdflgg15f9cvlx8cdmbd3y09d7i1dk421z28jlwzrs"; depends=[Rcpp zlibbioc]; };
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oncomix = derive2 { name="oncomix"; version="1.18.0"; sha256="0yj0p2vkph8qy1hhfv8nc15ac0z506xazzsmq6a7pvz5yqw7hxqc"; depends=[ggplot2 ggrepel mclust RColorBrewer SummarizedExperiment]; };
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oneSENSE = derive2 { name="oneSENSE"; version="1.18.0"; sha256="189zhz5glffh0q368mj8z7q7kvdpx2yl7xvwz5q20ckqj3xyyf10"; depends=[flowCore gplots plotly Rtsne scatterplot3d shiny shinyFiles webshot]; };
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@ -1765,7 +1765,7 @@ in with self; {
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pepXMLTab = derive2 { name="pepXMLTab"; version="1.30.0"; sha256="11fnm35cbnwy9l09mci9846xcv2mxvknv9hb1bs1i8381q8ysvws"; depends=[XML]; };
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periodicDNA = derive2 { name="periodicDNA"; version="1.6.0"; sha256="0ak5i5pqhjyz99lhbiqxjymsars3pajfwd2snzlyc7xd1fjxg06s"; depends=[BiocParallel Biostrings BSgenome cowplot GenomeInfoDb GenomicRanges ggplot2 IRanges magrittr rtracklayer S4Vectors zoo]; };
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pgca = derive2 { name="pgca"; version="1.20.0"; sha256="1mrn054flab2v18za40fhfxn691g3gq93p1ciyxfakbyb89ryi5x"; depends=[]; };
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phantasus = derive2 { name="phantasus"; version="1.15.8"; sha256="071s6mhm8bpbcnhbrfnxcha8pvf5i03ak09v56hkkgi9a5iwnwjg"; depends=[AnnotationDbi assertthat Biobase ccaPP curl data_table DESeq2 fgsea GEOquery ggplot2 gtable htmltools httpuv httr jsonlite limma Matrix opencpu pheatmap protolite rhdf5 Rook scales stringr svglite]; };
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phantasus = derive2 { name="phantasus"; version="1.16.2"; sha256="0r860hs25higr4crq1jf0s9a8pzrxbswdmz2zyx5bx0p1b78m6si"; depends=[AnnotationDbi assertthat Biobase ccaPP curl data_table DESeq2 fgsea GEOquery ggplot2 gtable htmltools httpuv httr jsonlite limma Matrix opencpu pheatmap protolite rhdf5 Rook scales stringr svglite]; };
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phenoTest = derive2 { name="phenoTest"; version="1.44.0"; sha256="0dm3h7ax83j3izcij7cdf8wg9cl4409vwnmzfbymf33y2l2z8csx"; depends=[annotate AnnotationDbi Biobase biomaRt BMA Category ellipse genefilter ggplot2 gplots GSEABase Heatplus hgu133a_db Hmisc hopach limma mgcv survival xtable]; };
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phenopath = derive2 { name="phenopath"; version="1.20.0"; sha256="114v90my05q89bgyjgl2ix62h3l4xcy96j2fncmpa89l7zax9fr2"; depends=[dplyr ggplot2 Rcpp SummarizedExperiment tibble tidyr]; };
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philr = derive2 { name="philr"; version="1.22.0"; sha256="1mj6mzl74dbpdhc5laiax5h20i0rh9n2rkip7vgwr5qc26a16kcw"; depends=[ape ggplot2 ggtree phangorn tidyr]; };
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@ -1781,7 +1781,7 @@ in with self; {
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plgem = derive2 { name="plgem"; version="1.68.0"; sha256="07zxflxcay17hxjw3wh5kfdwl2x8537csb18p1qzmyrkvscnja77"; depends=[Biobase MASS]; };
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plier = derive2 { name="plier"; version="1.66.0"; sha256="0zs053ih93klbdwz4gg8m5kizn9ifdccvgm21ddphv9jyn0sic4b"; depends=[affy Biobase]; };
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plotGrouper = derive2 { name="plotGrouper"; version="1.14.0"; sha256="1v8yjpavyz6gkm9wpv1ja3ifgdm25x7yw3rsb40py3bfz6wq50pr"; depends=[colourpicker dplyr egg ggplot2 ggpubr gridExtra gtable Hmisc magrittr readr readxl rlang scales shiny shinythemes stringr tibble tidyr]; };
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plotgardener = derive2 { name="plotgardener"; version="1.2.0"; sha256="0vz9x5lcpcczf130ryk0pw02xnrb9rsagmhx0x3pry7mz8xz3sdj"; depends=[curl data_table dplyr ggplotify IRanges plyranges purrr RColorBrewer Rcpp rlang strawr]; };
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plotgardener = derive2 { name="plotgardener"; version="1.2.6"; sha256="0fpkix2shy78bl8cjg9xhq4lhy9rlgqyp5msalzi3jip46784sa2"; depends=[curl data_table dplyr ggplotify IRanges plyranges purrr RColorBrewer Rcpp rlang strawr]; };
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plyranges = derive2 { name="plyranges"; version="1.16.0"; sha256="16af5v9k40sc152bgywkhzxbwx3gyljmn4whx0idfr58q5lafk90"; depends=[BiocGenerics dplyr GenomeInfoDb GenomicAlignments GenomicRanges IRanges magrittr rlang Rsamtools rtracklayer S4Vectors tidyselect]; };
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pmm = derive2 { name="pmm"; version="1.28.0"; sha256="1s2b4n91chjsplcmk8zj1sc8fm834vq1rygj10fvap9cnacc53pr"; depends=[lme4]; };
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pmp = derive2 { name="pmp"; version="1.8.0"; sha256="12bfbcvsxvlrv4znb7sy5ysmqr3rgpf24axcd5clhbw4xxsasak9"; depends=[ggplot2 impute matrixStats missForest pcaMethods reshape2 S4Vectors SummarizedExperiment]; };
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@ -1860,7 +1860,7 @@ in with self; {
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reconsi = derive2 { name="reconsi"; version="1.8.0"; sha256="0vpx9a9bwwnsgaxazmdggqvw1ap34xj30rshkq0imwfw8s1hagsq"; depends=[ggplot2 ks Matrix matrixStats phyloseq reshape2]; };
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recount = derive2 { name="recount"; version="1.22.0"; sha256="1mipj8nrihn7gmxn81l9bxv0rbr9zly7s3vfrbzimvg56iq8wrly"; depends=[BiocParallel derfinder downloader GenomeInfoDb GenomicRanges GEOquery IRanges RCurl rentrez rtracklayer S4Vectors SummarizedExperiment]; };
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recount3 = derive2 { name="recount3"; version="1.6.0"; sha256="0322vplaz77dmvkb7f2ybfgm5bidfq97zrprhvyn28zw2qllr8vg"; depends=[BiocFileCache data_table GenomicRanges Matrix R_utils RCurl rtracklayer S4Vectors sessioninfo SummarizedExperiment]; };
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recountmethylation = derive2 { name="recountmethylation"; version="1.6.0"; sha256="029zd94zvy5f2f634i2z7swp975znjb4l69x3wfhxj1fx6yi0pq7"; depends=[BiocFileCache HDF5Array IlluminaHumanMethylation450kmanifest minfi R_utils RCurl rhdf5 S4Vectors]; };
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recountmethylation = derive2 { name="recountmethylation"; version="1.6.1"; sha256="1k582mnq0vdjsz1jyb7h45p6klz9lc35law4x6ydjiv6z0wld55i"; depends=[BiocFileCache HDF5Array IlluminaHumanMethylation450kmanifest minfi R_utils RCurl rhdf5 S4Vectors]; };
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recoup = derive2 { name="recoup"; version="1.24.0"; sha256="1qrlhfrg991x0w5p4jlyra6wdvnqljiicckw0iqzybwp5xha8wkp"; depends=[BiocGenerics biomaRt Biostrings circlize ComplexHeatmap GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 httr IRanges Rsamtools RSQLite rtracklayer S4Vectors stringr]; };
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regionReport = derive2 { name="regionReport"; version="1.30.0"; sha256="1qqii65xvmj7fgsx45n6szpr0l3z6q2c9s76mx4977wq5rhx8w09"; depends=[BiocStyle DEFormats derfinder DESeq2 GenomeInfoDb GenomicRanges knitr knitrBootstrap RefManageR rmarkdown S4Vectors SummarizedExperiment]; };
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regioneR = derive2 { name="regioneR"; version="1.28.0"; sha256="11whi2v211xiz9s7cjl14d8vavlry2fmhvx12rma25wkjmhrpa3f"; depends=[Biostrings BSgenome GenomeInfoDb GenomicRanges IRanges memoise rtracklayer S4Vectors]; };
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@ -1884,8 +1884,8 @@ in with self; {
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rnaEditr = derive2 { name="rnaEditr"; version="1.6.0"; sha256="1js6a0y5hmkilsq1vgnkjk798z6dnz0acphgfq40p7i6182w1bx8"; depends=[BiocGenerics bumphunter corrplot GenomeInfoDb GenomicRanges IRanges logistf plyr S4Vectors survival]; };
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rnaseqcomp = derive2 { name="rnaseqcomp"; version="1.26.0"; sha256="1gpdlv980nid6nsjg1prahdxwp1a8ij00xgzf08ir4ywpvy61ilz"; depends=[RColorBrewer]; };
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roar = derive2 { name="roar"; version="1.32.0"; sha256="0zq1praf5h9294cvmrb06l3chx8v40xw2sfvhlnh1516x9sjkwfc"; depends=[BiocGenerics GenomeInfoDb GenomicAlignments GenomicRanges IRanges rtracklayer S4Vectors SummarizedExperiment]; };
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rols = derive2 { name="rols"; version="2.24.0"; sha256="05lf7nfh8rbybcw3pjpbnn4apa8fwna3nygkr6sbcm7j11q1cac2"; depends=[Biobase BiocGenerics httr jsonlite progress]; };
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ropls = derive2 { name="ropls"; version="1.28.0"; sha256="1i9g32mjknrd2lbz2nisc7nr0gk9byx9aik1i7xdwmq4ndxf8rf7"; depends=[Biobase MultiDataSet]; };
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rols = derive2 { name="rols"; version="2.24.2"; sha256="0c6n6bs5s9dv6j22yp0b38phpqwa7nx4ynv2gnsxvbiqqgk11c1k"; depends=[Biobase BiocGenerics httr jsonlite progress]; };
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ropls = derive2 { name="ropls"; version="1.28.2"; sha256="07gpx15r8c3wljiwxnff2zp7wxbhzz9r7njk8zg8hpy2q5qm3i6c"; depends=[Biobase MultiAssayExperiment MultiDataSet SummarizedExperiment]; };
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rprimer = derive2 { name="rprimer"; version="1.0.0"; sha256="040fy6zjvjjgz9syczvy8dpv02jnl3pv8vb75n40622z0c2hl1nx"; depends=[Biostrings bslib DT ggplot2 IRanges mathjaxr patchwork reshape2 S4Vectors shiny shinycssloaders shinyFeedback]; };
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rpx = derive2 { name="rpx"; version="2.4.0"; sha256="1y6pxvzga7yzgym1q5y4hmgyc9v30c574hj37a3wx9aanmjs78kw"; depends=[BiocFileCache curl jsonlite RCurl xml2]; };
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rqt = derive2 { name="rqt"; version="1.22.0"; sha256="0039sk0dx4d7fqc9yl0grwlv5k18sv08piqyc3fyp66302p38wrj"; depends=[car CompQuadForm glmnet Matrix metap pls ropls RUnit SummarizedExperiment]; };
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@ -1893,7 +1893,7 @@ in with self; {
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rrvgo = derive2 { name="rrvgo"; version="1.8.0"; sha256="1r90q18nhmzh45djbi1i5x3bcyzbybkp9d5j8i8yqxphs29sr5vx"; depends=[AnnotationDbi ggplot2 ggrepel GO_db GOSemSim pheatmap shiny tm treemap wordcloud]; };
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rsbml = derive2 { name="rsbml"; version="2.54.0"; sha256="1v11pspkml6xdsacgwxw8r4qdhbnn2h2sqgpm9aidaq9p2085b0v"; depends=[BiocGenerics graph]; };
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rsemmed = derive2 { name="rsemmed"; version="1.6.0"; sha256="0dw607kxcwv5dig5y3gja5916bpjki3bkphc7jxs79y9sl22zg4p"; depends=[dplyr igraph magrittr stringr]; };
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rtracklayer = derive2 { name="rtracklayer"; version="1.56.0"; sha256="1d9sak1xrrkcvj0q3vnp6w2k0nx2k2ajhsbq0dyb4nhcghp5w8fd"; depends=[BiocGenerics BiocIO Biostrings GenomeInfoDb GenomicAlignments GenomicRanges IRanges RCurl restfulr Rsamtools S4Vectors XML XVector zlibbioc]; };
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rtracklayer = derive2 { name="rtracklayer"; version="1.56.1"; sha256="10qy9s6253mgj871qfqn03i8yw10mz7id4cxfyf67qxczz2xmjls"; depends=[BiocGenerics BiocIO Biostrings GenomeInfoDb GenomicAlignments GenomicRanges IRanges RCurl restfulr Rsamtools S4Vectors XML XVector zlibbioc]; };
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runibic = derive2 { name="runibic"; version="1.18.0"; sha256="04a12w2hnybw5h27b7szd4v4r4p3z359xkrpqpqp9hmvbrx6apa6"; depends=[biclust Rcpp SummarizedExperiment testthat]; };
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sRACIPE = derive2 { name="sRACIPE"; version="1.12.0"; sha256="0q749j2pqhnmlx8d6vak3ig4ggqqwv74sfapfysbfg4n1v6cpkhp"; depends=[BiocGenerics ggplot2 gplots gridExtra htmlwidgets MASS RColorBrewer Rcpp reshape2 S4Vectors SummarizedExperiment umap visNetwork]; };
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sSNAPPY = derive2 { name="sSNAPPY"; version="1.0.0"; sha256="041lynrardz9z4yzy8bjv1w0ah4sjbkmx0wagfvxj7jhrikvky14"; depends=[BiocParallel dplyr edgeR ggplot2 ggraph graphite igraph magrittr org_Hs_eg_db plyr purrr Rcpp RcppArmadillo reshape2 rlang SummarizedExperiment tibble]; };
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@ -1901,7 +1901,7 @@ in with self; {
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safe = derive2 { name="safe"; version="3.36.0"; sha256="19hxp2zg48dmw1j5jsp2i9n6ccw4613i5bhi5wg6kld4wy8k496v"; depends=[AnnotationDbi Biobase SparseM]; };
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sagenhaft = derive2 { name="sagenhaft"; version="1.66.0"; sha256="0czbjc83df4xgavkqf4qvypcy0wzlzpdysjmyd189jqinagifzjy"; depends=[SparseM]; };
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sampleClassifier = derive2 { name="sampleClassifier"; version="1.20.0"; sha256="1gx76wcln8nxfm4h9klndi7rpzqpcci4h0fxqqhpsd0x19yw6rz2"; depends=[annotate e1071 ggplot2 MGFM MGFR]; };
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sangeranalyseR = derive2 { name="sangeranalyseR"; version="1.5.1"; sha256="1cy2nrrypvq3kah0q7bk3fl31syb9d3zssks8ljj6aiancwfm3jl"; depends=[ape BiocStyle Biostrings data_table DECIPHER DT excelR ggdendro gridExtra knitr logger openxlsx phangorn plotly reshape2 rmarkdown sangerseqR seqinr shiny shinycssloaders shinydashboard shinyjs shinyWidgets stringr zeallot]; };
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sangeranalyseR = derive2 { name="sangeranalyseR"; version="1.6.1"; sha256="0qp36w1mfwj0kzx055sc3gfyi0b86zahlsjvdiiclpwxh7wizkc4"; depends=[ape BiocStyle Biostrings data_table DECIPHER DT excelR ggdendro gridExtra knitr logger openxlsx phangorn plotly reshape2 rmarkdown sangerseqR seqinr shiny shinycssloaders shinydashboard shinyjs shinyWidgets stringr zeallot]; };
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sangerseqR = derive2 { name="sangerseqR"; version="1.32.0"; sha256="12rh6y38j66l21dlb1199imp4jwkpv19l306lj7qi7prcfwzhmmy"; depends=[Biostrings shiny]; };
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sarks = derive2 { name="sarks"; version="1.8.0"; sha256="1da5vxbf7r2yla1l1m5gcbqbka33c2ry7gwnmjixr6xlv9vs4209"; depends=[binom Biostrings cluster IRanges rJava]; };
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satuRn = derive2 { name="satuRn"; version="1.4.0"; sha256="0lqg5ha6k8wlqcrds0j4bflppqrl0q6q12h4l3k5w8kfpwy397d2"; depends=[BiocParallel boot ggplot2 limma locfdr Matrix pbapply SummarizedExperiment]; };
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@ -1945,7 +1945,7 @@ in with self; {
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scran = derive2 { name="scran"; version="1.24.0"; sha256="0xg7dl35915a65pmzkxdacsm4iqf97ayljdjljcvqx1ycmn7x68w"; depends=[beachmat BH BiocGenerics BiocParallel BiocSingular bluster DelayedArray DelayedMatrixStats dqrng edgeR igraph limma Matrix metapod Rcpp S4Vectors scuttle SingleCellExperiment statmod SummarizedExperiment]; };
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scruff = derive2 { name="scruff"; version="1.14.0"; sha256="0y5p27ih1v4qz47i83zvwwk1d4qkw6i9hwkfpdma3fw87ffxdy0q"; depends=[AnnotationDbi BiocGenerics BiocParallel Biostrings data_table GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggbio ggplot2 ggthemes plyr Rsamtools Rsubread rtracklayer S4Vectors scales ShortRead SingleCellExperiment stringdist SummarizedExperiment]; };
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scry = derive2 { name="scry"; version="1.8.0"; sha256="16mj21r91jy8ircdz8rfrdli9gjy0hrx90kf6ghs305d3d4dl193"; depends=[BiocSingular DelayedArray glmpca HDF5Array Matrix SingleCellExperiment SummarizedExperiment]; };
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scuttle = derive2 { name="scuttle"; version="1.6.0"; sha256="1l2vg6c8wpbspcrrp0jrq7pq23y9vj9921pr5wn0yxp8hb9ip4j2"; depends=[beachmat BiocGenerics BiocParallel DelayedArray DelayedMatrixStats GenomicRanges Matrix Rcpp S4Vectors SingleCellExperiment SummarizedExperiment]; };
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scuttle = derive2 { name="scuttle"; version="1.6.2"; sha256="0nnmq3wf436xaw4arc4y3ldvn6ilsg52xzbccmid0icb8z3y2kzn"; depends=[beachmat BiocGenerics BiocParallel DelayedArray DelayedMatrixStats GenomicRanges Matrix Rcpp S4Vectors SingleCellExperiment SummarizedExperiment]; };
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sechm = derive2 { name="sechm"; version="1.4.1"; sha256="1rimldsflmaa0ljrhi4am91hvkx6k8xvx5b0q3yl5ndblv2i6rvc"; depends=[circlize ComplexHeatmap matrixStats randomcoloR S4Vectors seriation SummarizedExperiment]; };
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segmentSeq = derive2 { name="segmentSeq"; version="2.30.0"; sha256="16ijs06ccm36z634qyrs3pjcnv0ssdzbvd4r76n55qq0mb10fgcq"; depends=[abind baySeq GenomeInfoDb GenomicRanges IRanges Rsamtools S4Vectors ShortRead]; };
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segmenter = derive2 { name="segmenter"; version="1.2.0"; sha256="1q3dx6j3d85f94ki67lga81d7nk0swy5y8ip3fab186i3amdlwjk"; depends=[bamsignals ChIPseeker chromhmmData ComplexHeatmap GenomicRanges IRanges S4Vectors SummarizedExperiment]; };
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@ -1961,11 +1961,11 @@ in with self; {
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seqbias = derive2 { name="seqbias"; version="1.44.0"; sha256="085nq6pf0bdn17wsbr5jnyy512v7rf67xff9rp5wz47mcifbv6rg"; depends=[Biostrings GenomicRanges Rhtslib]; };
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seqcombo = derive2 { name="seqcombo"; version="1.18.0"; sha256="1y8pv1zl0vv5ng9nl0rgsgig6k6n6v9jhmax7wgrplz056x1ha8p"; depends=[ggplot2 igraph yulab_utils]; };
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seqsetvis = derive2 { name="seqsetvis"; version="1.16.0"; sha256="0yzr1xcyhmziajj8c0v6gxsy5hz01i2ld0m4dvgx51f91gdv4q3p"; depends=[cowplot data_table eulerr GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 ggplotify IRanges limma pbapply pbmcapply png RColorBrewer Rsamtools rtracklayer S4Vectors UpSetR]; };
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sesame = derive2 { name="sesame"; version="1.14.0"; sha256="06izlyjbigsvm4f99raajqrl8fzwk5pb2rnv63zx8clr8gdba9sw"; depends=[BiocFileCache BiocParallel dplyr GenomeInfoDb GenomicRanges ggplot2 illuminaio IRanges MASS preprocessCore readr reshape2 S4Vectors sesameData stringr SummarizedExperiment tibble wheatmap]; };
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sesame = derive2 { name="sesame"; version="1.14.2"; sha256="1lpx2w21993i7jzwphf4hwl3d1da9qq6wcn8nr6rglfc23h0cj0i"; depends=[BiocFileCache BiocParallel dplyr GenomeInfoDb GenomicRanges ggplot2 illuminaio IRanges MASS preprocessCore readr reshape2 S4Vectors sesameData stringr SummarizedExperiment tibble wheatmap]; };
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sevenC = derive2 { name="sevenC"; version="1.16.0"; sha256="0gv319qrm37yrzvrv9ns0vsar18i0b94mgqbsnkw3122mzrlhfy1"; depends=[BiocGenerics boot data_table GenomeInfoDb GenomicRanges InteractionSet IRanges purrr readr rtracklayer S4Vectors]; };
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sevenbridges = derive2 { name="sevenbridges"; version="1.26.0"; sha256="170msiz4n1n16m3cddnw6jpwvh2j7y6gi6cvbzr4psqabynlvn7x"; depends=[curl data_table docopt httr jsonlite objectProperties S4Vectors stringr uuid yaml]; };
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shinyMethyl = derive2 { name="shinyMethyl"; version="1.32.0"; sha256="1636y3f9653l5dn4pyrq7kz54vjy2fmg4qrr9pav0215rfilgzyy"; depends=[BiocGenerics IlluminaHumanMethylation450kmanifest matrixStats minfi RColorBrewer shiny]; };
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shinyepico = derive2 { name="shinyepico"; version="1.4.0"; sha256="041agrbqd39f2ckq4bs4vd1k4cqahk268v07dqlirr5g6ki4lwgr"; depends=[data_table doParallel dplyr DT foreach GenomicRanges ggplot2 gplots heatmaply limma minfi plotly reshape2 rlang rmarkdown rtracklayer shiny shinycssloaders shinyjs shinythemes shinyWidgets statmod tidyr zip]; };
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shinyepico = derive2 { name="shinyepico"; version="1.4.2"; sha256="1pq6kmsq3b965vqc0y2aqniimwpv8i11af22qypcv0mhqk1xlx1m"; depends=[data_table doParallel dplyr DT foreach GenomicRanges ggplot2 gplots heatmaply limma minfi plotly reshape2 rlang rmarkdown rtracklayer shiny shinycssloaders shinyjs shinythemes shinyWidgets statmod tidyr zip]; };
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sigFeature = derive2 { name="sigFeature"; version="1.14.0"; sha256="0770hqhq7y1q3mknsfjh0x2rwlmm85wqhi7375bpj612npaqdc7m"; depends=[BiocParallel biocViews e1071 Matrix nlme openxlsx pheatmap RColorBrewer SparseM SummarizedExperiment]; };
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sigPathway = derive2 { name="sigPathway"; version="1.64.0"; sha256="1c2kwhbxgf66az7ssm2mab9n5x59zy4kxq8vblz5r9636xqaysif"; depends=[]; };
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siggenes = derive2 { name="siggenes"; version="1.70.0"; sha256="0amjqm2c8p1vjzx109p7n81wbsbx8rljwn6mbkl7dpi834im9d7l"; depends=[Biobase multtest scrime]; };
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@ -1974,7 +1974,7 @@ in with self; {
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signeR = derive2 { name="signeR"; version="1.22.0"; sha256="13jv0f90p462clwncp2ggky0n1xx4vaicak8712dnqzfzch04pzm"; depends=[BiocGenerics Biostrings class GenomeInfoDb GenomicRanges IRanges nloptr NMF PMCMRplus Rcpp RcppArmadillo VariantAnnotation]; };
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sigsquared = derive2 { name="sigsquared"; version="1.28.0"; sha256="13dvbl3s345yqmdxcrk19ql1asspgcc08p9sfyx1n6caamwg90a9"; depends=[Biobase survival]; };
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similaRpeak = derive2 { name="similaRpeak"; version="1.28.0"; sha256="14bkmfwwx0x8gz78bzyhfgy5rpvvafxq5z9r8knv4qj6hp1kalsh"; depends=[R6]; };
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simplifyEnrichment = derive2 { name="simplifyEnrichment"; version="1.6.0"; sha256="1g3kfa17p60jkk4l34vc5hdq83w082qsxbjvpqw7r9rdd8d79z2q"; depends=[AnnotationDbi BiocGenerics circlize clue cluster colorspace ComplexHeatmap digest GetoptLong GlobalOptions GO_db GOSemSim Matrix org_Hs_eg_db proxyC slam tm]; };
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simplifyEnrichment = derive2 { name="simplifyEnrichment"; version="1.6.1"; sha256="0qblgdxmr7zc981529cca3ykakql618q1im6gaxw8pwws5jgpyk6"; depends=[AnnotationDbi BiocGenerics circlize clue cluster colorspace ComplexHeatmap digest GetoptLong GlobalOptions GO_db GOSemSim Matrix org_Hs_eg_db proxyC slam tm]; };
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sincell = derive2 { name="sincell"; version="1.28.0"; sha256="152hlryc3xhkyp2v7fq20f0d04b2wvr09fl5p8fhiw1r0465vyab"; depends=[cluster entropy fastICA fields ggplot2 igraph MASS proxy Rcpp reshape2 Rtsne scatterplot3d statmod TSP]; };
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single = derive2 { name="single"; version="1.0.0"; sha256="1nx6cglidcmxznmvpkydj1lhgb2wyisl3yqqj0kfzbng2mxv6g0r"; depends=[BiocGenerics Biostrings dplyr GenomicAlignments IRanges reshape2 rlang Rsamtools stringr tidyr]; };
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singleCellTK = derive2 { name="singleCellTK"; version="2.6.0"; sha256="06hvxxdd8sdx8idgfqpnlxap7mq80asqgl5iq2paa1p6zvjk0w1b"; depends=[ape batchelor Biobase BiocParallel celda celldex circlize cluster colorspace colourpicker ComplexHeatmap cowplot data_table DelayedArray DelayedMatrixStats DESeq2 dplyr DropletUtils DT enrichR ExperimentHub fields fishpond generics ggplot2 ggplotify ggrepel ggtree gridExtra GSEABase GSVA GSVAdata igraph KernSmooth limma magrittr MAST Matrix matrixStats metap msigdbr multtest plotly plyr R_utils reshape2 reticulate rlang rmarkdown ROCR Rtsne S4Vectors scater scDblFinder scds scMerge scran scRNAseq scuttle Seurat shiny shinyalert shinycssloaders shinyjs SingleCellExperiment SingleR SoupX SummarizedExperiment sva TENxPBMCData tibble TrajectoryUtils TSCAN tximport VAM withr yaml zinbwave]; };
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@ -1991,7 +1991,7 @@ in with self; {
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snm = derive2 { name="snm"; version="1.44.0"; sha256="08vpzp7xr2w2qg1zcxqqj4wayik661cv2s5niivb7r82jxf6rm6i"; depends=[corpcor lme4]; };
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snpStats = derive2 { name="snpStats"; version="1.46.0"; sha256="0a5b5nqc7n965jk45ijwkzbn416ib4gfhp8xl39z8f2bdskip4a2"; depends=[BiocGenerics Matrix survival zlibbioc]; };
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soGGi = derive2 { name="soGGi"; version="1.28.0"; sha256="0hdqikcisva4blak5znwwv4xxvxxkg5n3jx0q4mhbqk7sp28p8vp"; depends=[BiocGenerics BiocParallel Biostrings chipseq GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 IRanges preprocessCore reshape2 Rsamtools rtracklayer S4Vectors SummarizedExperiment]; };
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sojourner = derive2 { name="sojourner"; version="1.10.0"; sha256="19gg70hjydxqj46ll6hanl3yvcpc9kmy65i1hh1w6yqph05xralb"; depends=[dplyr EBImage fitdistrplus ggplot2 gridExtra lattice MASS mclust minpack_lm mixtools mltools nls2 pixmap plyr R_matlab Rcpp reshape2 rlang sampSurf scales shiny shinyjs sp truncnorm]; };
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sojourner = derive2 { name="sojourner"; version="1.10.0"; sha256="19gg70hjydxqj46ll6hanl3yvcpc9kmy65i1hh1w6yqph05xralb"; depends=[dplyr EBImage fitdistrplus ggplot2 gridExtra lattice MASS mclust minpack_lm mixtools mltools nls2 pixmap plyr R_matlab Rcpp reshape2 rlang scales shiny shinyjs sp truncnorm]; };
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sparrow = derive2 { name="sparrow"; version="1.2.0"; sha256="0asmqfadqjc99dvrcdsz6jcvqkkqd5d3cf822jpf93ywk75a7gww"; depends=[babelgene BiocGenerics BiocParallel BiocSet checkmate circlize ComplexHeatmap data_table DelayedMatrixStats edgeR ggplot2 GSEABase irlba limma Matrix plotly viridis]; };
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sparseDOSSA = derive2 { name="sparseDOSSA"; version="1.20.0"; sha256="16wgj99i05s4gvv8i7k8ycdmyjs2bp6n61ahab0x10qhw823yy4s"; depends=[MASS MCMCpack optparse tmvtnorm]; };
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sparseMatrixStats = derive2 { name="sparseMatrixStats"; version="1.8.0"; sha256="0p12kay7p5zbfm2589wdx0n9jhgpf5fb2fsmkhn3p4ck4xcy13x2"; depends=[Matrix MatrixGenerics matrixStats Rcpp]; };
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@ -2039,7 +2039,7 @@ in with self; {
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synergyfinder = derive2 { name="synergyfinder"; version="3.4.0"; sha256="18z5gv73sz3hkxa3zdciwfbb1pl054mipvjs7mjhvz0s46w63pr8"; depends=[dplyr drc furrr future ggforce ggplot2 ggrepel gstat kriging lattice magrittr metR mice nleqslv pbapply plotly purrr reshape2 sp SpatialExtremes stringr tidyr tidyverse vegan]; };
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synlet = derive2 { name="synlet"; version="1.26.0"; sha256="0zygs6gskgddb68as4yh3bw1kjlsxk60rym1f6yxj5vzln0ka53c"; depends=[doBy dplyr ggplot2 magrittr RankProd RColorBrewer reshape2]; };
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systemPipeR = derive2 { name="systemPipeR"; version="2.2.2"; sha256="1yybbff29gwv6rm0nw4yjw73bbl5prfj8gj4zky917smjfd459im"; depends=[BiocGenerics Biostrings crayon GenomicRanges ggplot2 htmlwidgets magrittr Rsamtools S4Vectors ShortRead stringr SummarizedExperiment yaml]; };
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systemPipeShiny = derive2 { name="systemPipeShiny"; version="1.6.0"; sha256="0384wijbhqdrxyq11ma62613rxs6cccrqa3l38hhcx8pfnwgprnk"; depends=[assertthat bsplus crayon dplyr drawer DT ggplot2 glue htmltools magrittr openssl plotly R6 rlang RSQLite rstudioapi shiny shinyAce shinydashboard shinydashboardPlus shinyFiles shinyjqui shinyjs shinytoastr shinyWidgets spsComps spsUtil stringr styler tibble vroom yaml]; };
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systemPipeShiny = derive2 { name="systemPipeShiny"; version="1.6.1"; sha256="1b0x9vy7mkppf20c0i5p65wjicz12njx7in9w4vjqggvixbc9cjn"; depends=[assertthat bsplus crayon dplyr drawer DT ggplot2 glue htmltools magrittr openssl plotly R6 rlang RSQLite rstudioapi shiny shinyAce shinydashboard shinydashboardPlus shinyFiles shinyjqui shinyjs shinytoastr shinyWidgets spsComps spsUtil stringr styler tibble vroom yaml]; };
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systemPipeTools = derive2 { name="systemPipeTools"; version="1.4.0"; sha256="0zandgmzwj5b3hk8w60rmmc40hkpsvg9vynpix50hi81s8vwj26j"; depends=[ape DESeq2 dplyr DT GGally ggplot2 ggrepel ggtree glmpca magrittr pheatmap plotly Rtsne SummarizedExperiment tibble]; };
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tLOH = derive2 { name="tLOH"; version="1.4.0"; sha256="03ap5c7pznmflnlx7q9bwl8d64x68vz849ld6lxhm7j6wsva2c9m"; depends=[data_table dplyr GenomicRanges ggplot2 MatrixGenerics purrr scales VariantAnnotation]; };
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tRNA = derive2 { name="tRNA"; version="1.14.0"; sha256="140lpja0brw898is5xazxdz1h1agfzwwx9w63fhxacyx1ll43h41"; depends=[BiocGenerics Biostrings GenomicRanges ggplot2 IRanges Modstrings S4Vectors scales stringr Structstrings XVector]; };
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@ -2051,8 +2051,8 @@ in with self; {
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tenXplore = derive2 { name="tenXplore"; version="1.17.1"; sha256="1k8v0igw44c5fbj1dsjkda98v1c8y9sdw8mjarmy5axlrz3cpcbf"; depends=[AnnotationDbi matrixStats ontoProc org_Mm_eg_db restfulSE shiny SummarizedExperiment]; };
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ternarynet = derive2 { name="ternarynet"; version="1.40.0"; sha256="02r53h6224f8jwwvnv1n09s8i8akhq2qf562crq14m8qk5xw4scf"; depends=[BiocParallel igraph]; };
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terraTCGAdata = derive2 { name="terraTCGAdata"; version="1.0.0"; sha256="16sc6n1cgrxr425024k37vzy1n2pij8n7lzxq383r73wyp5z3zkc"; depends=[AnVIL BiocFileCache dplyr GenomicRanges MultiAssayExperiment RaggedExperiment readr S4Vectors TCGAutils tidyr]; };
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tidySingleCellExperiment = derive2 { name="tidySingleCellExperiment"; version="1.6.0"; sha256="0jpw14qvi184fdawhif6b32c3ljm1g5wwf0g0ii9r8y0cf7z4bnl"; depends=[cli dplyr ellipsis fansi ggplot2 lifecycle magrittr pillar plotly purrr rlang S4Vectors SingleCellExperiment stringr SummarizedExperiment tibble tidyr tidyselect ttservice]; };
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tidySummarizedExperiment = derive2 { name="tidySummarizedExperiment"; version="1.6.0"; sha256="15w62bwfllfhscyxs56am58qhmmyh1hmwjc9axlmvxa2k9pvishw"; depends=[cli dplyr ellipsis fansi ggplot2 lifecycle magrittr pillar plotly purrr rlang S4Vectors stringr SummarizedExperiment tibble tidyr tidyselect]; };
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tidySingleCellExperiment = derive2 { name="tidySingleCellExperiment"; version="1.6.3"; sha256="1b90n9sirpff8dh8kh8m2p4lnpfpqfh0zwvhpk5ymnw7j7x1vw7n"; depends=[cli dplyr ellipsis fansi ggplot2 lifecycle magrittr pillar plotly purrr rlang S4Vectors SingleCellExperiment stringr SummarizedExperiment tibble tidyr tidyselect ttservice vctrs]; };
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tidySummarizedExperiment = derive2 { name="tidySummarizedExperiment"; version="1.6.1"; sha256="0y30479w9nim6yap55fcg99qi4599rnliacqaiq693qwnrglksmg"; depends=[cli dplyr ellipsis fansi ggplot2 lifecycle magrittr pillar plotly purrr rlang S4Vectors stringr SummarizedExperiment tibble tidyr tidyselect vctrs]; };
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tidybulk = derive2 { name="tidybulk"; version="1.8.0"; sha256="02dgny3zshn1g2lpr2s888yg230q6impi8dffr3x9c8yjak213xp"; depends=[dplyr GenomicRanges lifecycle magrittr preprocessCore purrr readr rlang scales stringi stringr SummarizedExperiment tibble tidyr tidyselect]; };
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tigre = derive2 { name="tigre"; version="1.50.0"; sha256="0a4nn8q6iz20xfpwjvdp387cc3w0wdd9rpn6p8gh3dkqh8wsnggd"; depends=[annotate AnnotationDbi Biobase BiocGenerics DBI gplots RSQLite]; };
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tilingArray = derive2 { name="tilingArray"; version="1.74.0"; sha256="17n30c0nybsqvmm920zfxfx82yz0afnv1p14jcrnhf3qi9ipdjna"; depends=[affy Biobase genefilter pixmap RColorBrewer strucchange vsn]; };
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@ -2065,7 +2065,7 @@ in with self; {
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topGO = derive2 { name="topGO"; version="2.48.0"; sha256="125r42ymk1irjmwk4sywjkcshs71s26p3zsvryfdvf56k5w162v6"; depends=[AnnotationDbi Biobase BiocGenerics DBI GO_db graph lattice matrixStats SparseM]; };
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topconfects = derive2 { name="topconfects"; version="1.12.0"; sha256="0v1cq7gvbwdqxczmy5vrw8yqk7h1bvx3rils4pkv7w9nhqps5g4k"; depends=[assertthat ggplot2]; };
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topdownr = derive2 { name="topdownr"; version="1.18.0"; sha256="1qrjgbs2lh851d22bcl75574jnyc554aqqxb34zdnpvpwavaqaya"; depends=[Biobase BiocGenerics Biostrings ggplot2 Matrix MSnbase mzR ProtGenerics S4Vectors]; };
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trackViewer = derive2 { name="trackViewer"; version="1.32.0"; sha256="0mrn514509924bs36fbdkk45vid19ldpwfyknagb8jhqdkqdngry"; depends=[AnnotationDbi BiocGenerics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges graph grImport Gviz htmlwidgets InteractionSet IRanges plotrix Rcpp Rgraphviz rhdf5 Rsamtools rtracklayer S4Vectors scales]; };
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trackViewer = derive2 { name="trackViewer"; version="1.32.1"; sha256="0hifh15z5d83qmrvh3kpi8i18dfqqfj6kn4kqkkcyxbfm1yx62h1"; depends=[AnnotationDbi BiocGenerics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges graph grImport Gviz htmlwidgets InteractionSet IRanges plotrix Rcpp Rgraphviz rhdf5 Rsamtools rtracklayer S4Vectors scales]; };
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tracktables = derive2 { name="tracktables"; version="1.30.0"; sha256="0xv4n8avwls10dk2kn2mhjq69cfqkackdn1jdz85xq5z42qnkl10"; depends=[GenomicRanges IRanges RColorBrewer Rsamtools stringr tractor_base XML XVector]; };
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tradeSeq = derive2 { name="tradeSeq"; version="1.10.0"; sha256="0v9nqxrwa69qhmyaicn2vvs8haha4kzs93iqim306331vadp9qm0"; depends=[Biobase BiocParallel edgeR ggplot2 igraph magrittr MASS Matrix matrixStats mgcv pbapply princurve RColorBrewer S4Vectors SingleCellExperiment slingshot SummarizedExperiment tibble TrajectoryUtils viridis]; };
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transcriptR = derive2 { name="transcriptR"; version="1.24.0"; sha256="1zc6aasd5nzwl9jxr0rdriiq85adqdbfi5b9m3jyf69pa71sgy03"; depends=[BiocGenerics caret chipseq e1071 GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 IRanges pROC reshape2 Rsamtools rtracklayer S4Vectors]; };
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@ -2077,7 +2077,7 @@ in with self; {
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traviz = derive2 { name="traviz"; version="1.2.0"; sha256="1y2gckk7nm1yb8qv1llkal3mzmdk11kgmdagflymhla4nx2gdgay"; depends=[Biobase ggplot2 mgcv princurve RColorBrewer rgl SingleCellExperiment slingshot SummarizedExperiment viridis]; };
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treeio = derive2 { name="treeio"; version="1.20.0"; sha256="1hc5m0b2qqxrh3z0inny2jizrpn9d4yn9pn3k1h18xb4ggyijyla"; depends=[ape dplyr jsonlite magrittr rlang tibble tidytree]; };
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treekoR = derive2 { name="treekoR"; version="1.4.0"; sha256="0sd1vk1hzvma0644p8wz4037gmm5wpf1d8n22fa0d5m7c97qijrl"; depends=[ape data_table diffcyt dplyr edgeR ggiraph ggplot2 ggtree hopach lme4 multcomp patchwork SingleCellExperiment tidyr]; };
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trena = derive2 { name="trena"; version="1.18.0"; sha256="02xhjy1nzjd7lgawqkn3vj3llg1fwl0nisapxmai7yl2lfajhia6"; depends=[AnnotationDbi biomaRt Biostrings BSgenome BSgenome_Hsapiens_UCSC_hg19 BSgenome_Hsapiens_UCSC_hg38 BSgenome_Mmusculus_UCSC_mm10 DBI GenomicRanges glmnet lassopv MotifDb org_Hs_eg_db randomForest RMySQL RPostgreSQL RSQLite SNPlocs_Hsapiens_dbSNP150_GRCh38 vbsr WGCNA xgboost]; };
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trena = derive2 { name="trena"; version="1.18.0"; sha256="02xhjy1nzjd7lgawqkn3vj3llg1fwl0nisapxmai7yl2lfajhia6"; depends=[AnnotationDbi biomaRt Biostrings BSgenome BSgenome_Hsapiens_UCSC_hg19 BSgenome_Hsapiens_UCSC_hg38 BSgenome_Mmusculus_UCSC_mm10 DBI GenomicRanges glmnet lassopv MotifDb org_Hs_eg_db randomForest RMySQL RPostgreSQL RSQLite SNPlocs_Hsapiens_dbSNP150_GRCh38 WGCNA xgboost]; };
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tricycle = derive2 { name="tricycle"; version="1.4.0"; sha256="0bjkajcz6xcfak6071d0ihakrvgf7s0pmkn6vqkjd6yxbfld7zln"; depends=[AnnotationDbi circular dplyr GenomicRanges ggnewscale ggplot2 IRanges RColorBrewer S4Vectors scater scattermore SingleCellExperiment SummarizedExperiment]; };
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trigger = derive2 { name="trigger"; version="1.42.0"; sha256="09gbchwpifx5dkmw3irshb63jl22fn2sxsj450krqjjq1gjq1xhx"; depends=[corpcor qtl qvalue sva]; };
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trio = derive2 { name="trio"; version="3.34.0"; sha256="1d6gwzx99np8yrsmqnn23s94ib6k41290sv2h4nmzblsidsimlbs"; depends=[LogicReg siggenes survival]; };
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@ -2095,7 +2095,7 @@ in with self; {
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uSORT = derive2 { name="uSORT"; version="1.22.0"; sha256="1fq9zqa0kgdzvc0bhr60kqkl27b5y525czfm0w7qmbv3a832mhhd"; depends=[Biobase BiocGenerics cluster fpc gplots igraph Matrix monocle plyr RANN RSpectra VGAM]; };
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uncoverappLib = derive2 { name="uncoverappLib"; version="1.6.0"; sha256="0r0vgi7pq93vpw7mcqw96ixfgkhwllw16v20jsk3v27jx5gvr31c"; depends=[BiocFileCache BSgenome_Hsapiens_UCSC_hg19 BSgenome_Hsapiens_UCSC_hg38 condformat DT EnsDb_Hsapiens_v75 EnsDb_Hsapiens_v86 GenomicRanges Gviz Homo_sapiens markdown openxlsx org_Hs_eg_db OrganismDbi processx rappdirs rlist Rsamtools S4Vectors shiny shinyBS shinycssloaders shinyjs shinyWidgets stringr TxDb_Hsapiens_UCSC_hg19_knownGene TxDb_Hsapiens_UCSC_hg38_knownGene]; };
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unifiedWMWqPCR = derive2 { name="unifiedWMWqPCR"; version="1.32.0"; sha256="1skfs94a6bv05c844zf5vfqw1fbgxyppgdnckdbhxg2a2470a4wh"; depends=[BiocGenerics HTqPCR]; };
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universalmotif = derive2 { name="universalmotif"; version="1.14.0"; sha256="0n2msyyy1xhapkd66j4xwabg4qfd62l01p1nmafjwifnjsx45xvp"; depends=[BiocGenerics Biostrings ggplot2 IRanges MASS Rcpp RcppThread rlang S4Vectors yaml]; };
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universalmotif = derive2 { name="universalmotif"; version="1.14.1"; sha256="1sm54z8aq3534qjsa19wychhwcvwnjlkydmiqqvidiiwcxwqpjsr"; depends=[BiocGenerics Biostrings ggplot2 IRanges MASS Rcpp RcppThread rlang S4Vectors yaml]; };
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updateObject = derive2 { name="updateObject"; version="1.0.0"; sha256="0ng927m9hrmwlnx02pm35b5173a0wx1b2k54gww9xc1pz9b5zp24"; depends=[BiocGenerics digest S4Vectors]; };
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variancePartition = derive2 { name="variancePartition"; version="1.26.0"; sha256="0wk1xql8b0gxyrqz9hs54xvmp7qdw9b8jnv88p4vgv061iwyk7wv"; depends=[aod Biobase BiocParallel doParallel foreach ggplot2 gplots iterators limma lme4 lmerTest MASS Matrix pbkrtest progress Rdpack reshape2 RhpcBLASctl rlang scales]; };
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vbmp = derive2 { name="vbmp"; version="1.64.0"; sha256="02xxvam2dmhhqvm30gxh2v16894qbqha1mc7bl78gq5sc067yr0n"; depends=[]; };
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@ -2123,7 +2123,7 @@ in with self; {
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yamss = derive2 { name="yamss"; version="1.22.0"; sha256="1lcfxw73cxvpy3bnq28pxdy5128mpq5xklsa0mzxdjyqc4g55hy8"; depends=[BiocGenerics data_table EBImage IRanges limma Matrix mzR S4Vectors SummarizedExperiment]; };
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yarn = derive2 { name="yarn"; version="1.22.0"; sha256="0z5202pqq02fwm8qf1g36004k7sv668s1xacbpr1cvw5sl452lbg"; depends=[Biobase biomaRt downloader edgeR gplots limma matrixStats preprocessCore quantro RColorBrewer readr]; };
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zFPKM = derive2 { name="zFPKM"; version="1.18.0"; sha256="1h7g553rgb5mkmmsp8dyqqs9n9x17xmmcg3iijhb54nyrr2j1mji"; depends=[checkmate dplyr ggplot2 SummarizedExperiment tidyr]; };
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zellkonverter = derive2 { name="zellkonverter"; version="1.6.0"; sha256="19rc3cjwqpazrwq6hx0iqhy9irzwn4n830ninjr46wfqc74bknj0"; depends=[basilisk cli DelayedArray Matrix reticulate S4Vectors SingleCellExperiment SummarizedExperiment]; };
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zellkonverter = derive2 { name="zellkonverter"; version="1.6.3"; sha256="0l6v7a2zyxpq2w3vm85z439ldi3ld3pkc3wx95a1vxzbr31cpdzz"; depends=[basilisk cli DelayedArray Matrix reticulate S4Vectors SingleCellExperiment SummarizedExperiment]; };
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zinbwave = derive2 { name="zinbwave"; version="1.18.0"; sha256="0vpz721sciw5b4ypxj5lj8p53gwkpfwlwkn6k3y8i65zg80p1g6i"; depends=[BiocParallel edgeR genefilter Matrix SingleCellExperiment softImpute SummarizedExperiment]; };
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zlibbioc = derive2 { name="zlibbioc"; version="1.42.0"; sha256="0w0y9jixdk6akmasn55g9g0nhlh93hbca5bwx5w1fypnvqrqpxzv"; depends=[]; };
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ABAEnrichment = derive2 { name="ABAEnrichment"; version="1.24.0"; sha256="1sp3f72rzlr822dxx42bswynrwwfx6f520hdhfdikqp13p2y4044"; depends=[ABAData data_table GOfuncR gplots gtools Rcpp]; broken = true; };
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