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R: update CRAN and Bioconductor package sets

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Closes https://github.com/NixOS/nixpkgs/pull/57423.
wip/yesman
Alex Branham 5 years ago committed by Peter Simons
parent 1e354a7e40
commit 8dcba2b842
3 changed files with 1125 additions and 963 deletions
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  1. 166
      pkgs/development/r-modules/bioc-packages.nix
  2. 1921
      pkgs/development/r-modules/cran-packages.nix
  3. 1
      pkgs/development/r-modules/default.nix

166
pkgs/development/r-modules/bioc-packages.nix generated
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@ -40,7 +40,7 @@ in with self; {
AnnotationFilter = derive2 { name="AnnotationFilter"; version="1.6.0"; sha256="0wrr10cxjzmxx46vjzq2nsf6xlqz1sqwx4xm0sk3d77ff8wmph4x"; depends=[GenomicRanges lazyeval]; };
AnnotationForge = derive2 { name="AnnotationForge"; version="1.24.0"; sha256="13yvhf3yskmvhs8szs6rkw93h81h5xqa3h19h91pp6nprhc8s3ll"; depends=[AnnotationDbi Biobase BiocGenerics DBI RCurl RSQLite S4Vectors XML]; };
AnnotationFuncs = derive2 { name="AnnotationFuncs"; version="1.32.0"; sha256="1x11mfabh7kbp39y5rkmrpjkaawx7ab5anfmciamrmrcw1kddbss"; depends=[AnnotationDbi DBI]; };
AnnotationHub = derive2 { name="AnnotationHub"; version="2.14.3"; sha256="04qfr7jmmp8h2c9q62fk1izild9cs03kjilz4k4anvg56ddm5v77"; depends=[AnnotationDbi BiocGenerics BiocManager curl httr interactiveDisplayBase RSQLite S4Vectors yaml]; };
AnnotationHub = derive2 { name="AnnotationHub"; version="2.14.4"; sha256="18v2mk395svq3c19wzi6bjwjfnmrvjqkzmj7cmaji7rx4xdgz6ck"; depends=[AnnotationDbi BiocGenerics BiocManager curl httr interactiveDisplayBase RSQLite S4Vectors yaml]; };
AnnotationHubData = derive2 { name="AnnotationHubData"; version="1.12.0"; sha256="1xim76sxldx70h13fpkhz7fxr5rcq0gp7558w4v1iqjjzd4gp3mh"; depends=[AnnotationDbi AnnotationForge AnnotationHub Biobase BiocGenerics BiocManager biocViews Biostrings DBI futile_logger GenomeInfoDb GenomicFeatures GenomicRanges IRanges jsonlite OrganismDbi rBiopaxParser RCurl Rsamtools RSQLite rtracklayer S4Vectors XML]; };
ArrayExpress = derive2 { name="ArrayExpress"; version="1.42.0"; sha256="1a61miwsyqghmqnfnfpd7b0p712mz9cpcrq00p9b7jr8j4jd5vla"; depends=[Biobase limma oligo XML]; };
ArrayExpressHTS = derive2 { name="ArrayExpressHTS"; version="1.32.1"; sha256="0gv3f1ynyl52ab7zvmfi9s34ns6nwqyayh5imv6b31l92rw5ifdm"; depends=[Biobase BiocGenerics biomaRt Biostrings bitops DESeq edgeR GenomicRanges Hmisc IRanges R2HTML RColorBrewer rJava Rsamtools sampling sendmailR ShortRead snow svMisc XML]; };
@ -95,7 +95,7 @@ in with self; {
BiocInstaller = derive2 { name="BiocInstaller"; version="1.32.1"; sha256="1s1f9qhyf3mc73ir25x2zlgi9hf45a37lg4z8fbva4i21hqisgsl"; depends=[]; };
BiocNeighbors = derive2 { name="BiocNeighbors"; version="1.0.0"; sha256="1fsb96acidlxwf0h65xv7fnwdi58ckmq00gmwykrlawh88wgn1ll"; depends=[BiocParallel Rcpp RcppAnnoy S4Vectors]; };
BiocOncoTK = derive2 { name="BiocOncoTK"; version="1.2.1"; sha256="0w0hqdyv580j2lxp0ma74swi0cmzf6z6v5zqnhss8qawmm90cc9x"; depends=[bigrquery ComplexHeatmap DBI dplyr DT GenomicFeatures GenomicRanges ggplot2 httr IRanges magrittr rjson S4Vectors shiny SummarizedExperiment]; };
BiocParallel = derive2 { name="BiocParallel"; version="1.16.5"; sha256="1164dk0fajb2vrkfpcjs11055qf1cs4vvbnq0aqdaaf2p4lyx41l"; depends=[BH futile_logger snow]; };
BiocParallel = derive2 { name="BiocParallel"; version="1.16.6"; sha256="1iv2xzm6lz371z0llhcxl8hmc5jfw0hjwnf1qc8d7jk9djgcaks2"; depends=[BH futile_logger snow]; };
BiocPkgTools = derive2 { name="BiocPkgTools"; version="1.0.3"; sha256="0mfxcabkdxsbkk1j3kncn5jhm08b0zi1jjsz7ajkhhw7c9w85gvm"; depends=[BiocManager dplyr DT gh htmltools htmlwidgets httr igraph jsonlite readr rex rvest stringr tibble tidyr xml2]; };
BiocSklearn = derive2 { name="BiocSklearn"; version="1.4.0"; sha256="08a1jaxhqaxqrhbgkm11isi3d83sbpfjh02nki7rbwffcjim3fy0"; depends=[BBmisc knitr reticulate SummarizedExperiment]; };
BiocStyle = derive2 { name="BiocStyle"; version="2.10.0"; sha256="01lm8xljilj666fcl3wnw82dxkcxnlr294lddr553rm8xr5nwg31"; depends=[BiocManager bookdown knitr rmarkdown yaml]; };
@ -140,7 +140,7 @@ in with self; {
CNVPanelizer = derive2 { name="CNVPanelizer"; version="1.14.0"; sha256="0fh94iv66li3zsnadxyxwzhs1jcz63vpmc6khp0srac2kzvc1kcs"; depends=[exomeCopy foreach GenomeInfoDb GenomicRanges ggplot2 gplots IRanges NOISeq openxlsx plyr reshape2 Rsamtools S4Vectors shiny shinyFiles shinyjs stringr testthat]; };
CNVrd2 = derive2 { name="CNVrd2"; version="1.20.0"; sha256="10141xwwkzrkgkad8x5y1ha779b47vp7b2qk32hgw19ys4lraj79"; depends=[DNAcopy ggplot2 gridExtra IRanges rjags Rsamtools VariantAnnotation]; };
CNVtools = derive2 { name="CNVtools"; version="1.76.0"; sha256="0xmqqq3j3xxm1pnldw6l3vnww9lfjlghvkrfzfbwxmq8gkxmyzji"; depends=[survival]; };
COCOA = derive2 { name="COCOA"; version="1.0.1"; sha256="1j53vvkh5y8icmzx7p6i33jw227wxdgsddqlb7wzjpdhv7x55c1j"; depends=[Biobase BiocGenerics ComplexHeatmap data_table GenomicRanges ggplot2 IRanges MIRA S4Vectors tidyr]; };
COCOA = derive2 { name="COCOA"; version="1.0.2"; sha256="1y7y3zjzpljfqdhal87xir9z50xg8p96n0yx98qz1lqairbdkcpj"; depends=[Biobase BiocGenerics ComplexHeatmap data_table GenomicRanges ggplot2 IRanges MIRA S4Vectors tidyr]; };
CODEX = derive2 { name="CODEX"; version="1.14.1"; sha256="0k8x1k1m11r69dbzrxqx9b1pqi5x3pf1cxyf5j4hz7qsk8fncsnq"; depends=[Biostrings BSgenome_Hsapiens_UCSC_hg19 GenomeInfoDb IRanges Rsamtools S4Vectors]; };
COHCAP = derive2 { name="COHCAP"; version="1.28.1"; sha256="1zn0skpi7h2nws877bj1van3358cmh88prvj9691kwcwj47h1zny"; depends=[BH COHCAPanno gplots RColorBrewer Rcpp RcppArmadillo WriteXLS]; };
COMPASS = derive2 { name="COMPASS"; version="1.20.1"; sha256="0jhi9dhyfdnc9fmybj2q9vcshkikn9rhcdzfr9hi2jizh7pa4w8z"; depends=[abind BiocStyle clue data_table dplyr knitr magrittr pdist plyr RColorBrewer Rcpp reshape2 rlang rmarkdown scales tidyr]; };
@ -156,8 +156,8 @@ in with self; {
CancerInSilico = derive2 { name="CancerInSilico"; version="2.2.1"; sha256="1irbgmwfpsjyl8an06qs7x0nh4jrljhklkm3ak2sd13fgg88j73s"; depends=[BH Rcpp]; };
CancerMutationAnalysis = derive2 { name="CancerMutationAnalysis"; version="1.24.0"; sha256="10768i5ijrwr7hcshk60r5w6ckqacqk3f9jhs3qkm2ic0g47vgwb"; depends=[AnnotationDbi limma qvalue]; };
CancerSubtypes = derive2 { name="CancerSubtypes"; version="1.8.0"; sha256="1cg1im5p53n5afz0pzfg7l7wp6lm8cl0dr5x8di62va71n9qdk77"; depends=[cluster ConsensusClusterPlus iCluster impute limma NMF sigclust SNFtool survival]; };
Cardinal = derive2 { name="Cardinal"; version="2.0.3"; sha256="0i6bihd6g89841kwjrdawh99c79jm8nxpwrbcjw7yzr3jx440h81"; depends=[Biobase BiocGenerics BiocParallel dplyr EBImage irlba lattice magrittr matter ProtGenerics S4Vectors signal sp]; };
Category = derive2 { name="Category"; version="2.48.0"; sha256="1jdm83bwdfhpfm1y6hwgvxzj6l83h1bdkqv23799kzywnwm016kv"; depends=[annotate AnnotationDbi Biobase BiocGenerics DBI genefilter graph GSEABase Matrix RBGL]; };
Cardinal = derive2 { name="Cardinal"; version="2.0.4"; sha256="1119r8993msnldilkp7qv3mslbbv3bfypidnm52cl9ybznlj757r"; depends=[Biobase BiocGenerics BiocParallel dplyr EBImage irlba lattice magrittr matter ProtGenerics S4Vectors signal sp]; };
Category = derive2 { name="Category"; version="2.48.1"; sha256="18rsxlwa1l06i635cnznb9b2zssqcgb71pihky29gl2gwp7a654b"; depends=[annotate AnnotationDbi Biobase BiocGenerics DBI genefilter graph GSEABase Matrix RBGL]; };
CausalR = derive2 { name="CausalR"; version="1.14.1"; sha256="0v4k8nbxjf9q092d029pvpy1f29zby8j60b89x559cr2m78zw870"; depends=[igraph]; };
CellMapper = derive2 { name="CellMapper"; version="1.8.0"; sha256="0qaw5pf3lgdkfcki0z2hp9g0b07j2khinwh9r0ajvji4j7hiwrw5"; depends=[S4Vectors]; };
CellNOptR = derive2 { name="CellNOptR"; version="1.28.1"; sha256="0ygpryc9sbj031lznlmhr23vgdqgyyyzjx6zbyv2nx703x9vrj3l"; depends=[ggplot2 graph hash RBGL RCurl Rgraphviz XML]; };
@ -167,7 +167,7 @@ in with self; {
ChAMP = derive2 { name="ChAMP"; version="2.12.4"; sha256="197b3k61panvxw0vxf8qjj8l86q95mf9al055scpcf7sc6xwz0db"; depends=[bumphunter ChAMPdata combinat dendextend DMRcate DNAcopy doParallel FEM GenomicRanges globaltest goseq Hmisc Illumina450ProbeVariants_db IlluminaHumanMethylation450kmanifest IlluminaHumanMethylationEPICanno_ilm10b2_hg19 IlluminaHumanMethylationEPICmanifest illuminaio impute isva kpmt limma marray matrixStats minfi missMethyl plotly plyr preprocessCore prettydoc quadprog qvalue RColorBrewer rmarkdown RPMM shiny shinythemes sva wateRmelon]; };
ChIC = derive2 { name="ChIC"; version="1.2.0"; sha256="190jc1k318bk1xh93h726bxl0711qzn672lri3lwsrbjm76w8m1g"; depends=[BiocGenerics caret caTools ChIC_data GenomicRanges IRanges progress S4Vectors spp]; };
ChIPComp = derive2 { name="ChIPComp"; version="1.12.0"; sha256="1sypdsvwzssraanlhddhzpf9p0xs3qlflc0hp7yfbp0aplsifx85"; depends=[BiocGenerics BSgenome_Hsapiens_UCSC_hg19 BSgenome_Mmusculus_UCSC_mm9 GenomeInfoDb GenomicRanges IRanges limma Rsamtools rtracklayer S4Vectors]; };
ChIPQC = derive2 { name="ChIPQC"; version="1.18.1"; sha256="15pzxskrlskdib0pp7xacr90k54m8c1k5w334z86km4yndjpffpp"; depends=[Biobase BiocGenerics BiocParallel chipseq DiffBind GenomicAlignments GenomicFeatures GenomicRanges ggplot2 gtools IRanges Nozzle_R1 reshape2 Rsamtools S4Vectors TxDb_Celegans_UCSC_ce6_ensGene TxDb_Dmelanogaster_UCSC_dm3_ensGene TxDb_Hsapiens_UCSC_hg18_knownGene TxDb_Hsapiens_UCSC_hg19_knownGene TxDb_Mmusculus_UCSC_mm10_knownGene TxDb_Mmusculus_UCSC_mm9_knownGene TxDb_Rnorvegicus_UCSC_rn4_ensGene]; };
ChIPQC = derive2 { name="ChIPQC"; version="1.18.2"; sha256="0khm2y36f92zpwqcqrd8jkrsbgfcir70dwi8zk7pq0hpbpnpl0bm"; depends=[Biobase BiocGenerics BiocParallel chipseq DiffBind GenomicAlignments GenomicFeatures GenomicRanges ggplot2 gtools IRanges Nozzle_R1 reshape2 Rsamtools S4Vectors TxDb_Celegans_UCSC_ce6_ensGene TxDb_Dmelanogaster_UCSC_dm3_ensGene TxDb_Hsapiens_UCSC_hg18_knownGene TxDb_Hsapiens_UCSC_hg19_knownGene TxDb_Mmusculus_UCSC_mm10_knownGene TxDb_Mmusculus_UCSC_mm9_knownGene TxDb_Rnorvegicus_UCSC_rn4_ensGene]; };
ChIPSeqSpike = derive2 { name="ChIPSeqSpike"; version="1.2.1"; sha256="0cy2099pc3vcjw47xigiq7qs8czfgaizlqyb5hy4j1lpr5c8qpia"; depends=[BiocGenerics corrplot GenomicRanges ggplot2 IRanges LSD Rsamtools rtracklayer S4Vectors seqplots stringr]; };
ChIPXpress = derive2 { name="ChIPXpress"; version="1.26.0"; sha256="1b5ss7s8chjm8zgpxkwmghgf2dh1xn225y1qfad838gs0d2rmd5h"; depends=[affy biganalytics bigmemory Biobase ChIPXpressData frma GEOquery]; };
ChIPanalyser = derive2 { name="ChIPanalyser"; version="1.4.0"; sha256="115ycr6s5lb9888sz9xxdsip22vnbj1gfavrm61ks12rqf0ch2b6"; depends=[BiocManager Biostrings BSgenome GenomeInfoDb GenomicRanges IRanges RcppRoll ROCR rtracklayer S4Vectors]; };
@ -180,13 +180,13 @@ in with self; {
ChemmineR = derive2 { name="ChemmineR"; version="3.34.1"; sha256="0pzvwaycvz61156ypqf24a42nhhmlhx2hccyra3g0jm97adm69iw"; depends=[base64enc BH BiocGenerics DBI digest DT ggplot2 gridExtra png Rcpp RCurl rjson rsvg]; };
Chicago = derive2 { name="Chicago"; version="1.10.1"; sha256="0m3fv8qgxaysnc02ndmk0bx0rk8ly02nivhn0hzgdh6vbrgqgzdr"; depends=[data_table Delaporte Hmisc MASS matrixStats]; };
ChromHeatMap = derive2 { name="ChromHeatMap"; version="1.36.0"; sha256="0ah133mzrwxdhfazpw41h2h0bz555al9yjlyhahm249d4wbdzr8d"; depends=[annotate AnnotationDbi Biobase BiocGenerics GenomicRanges IRanges rtracklayer]; };
ClassifyR = derive2 { name="ClassifyR"; version="2.2.5"; sha256="1kgzkgj484l3c369qhiysnj2zl4sjavbg263jq2q7ynk54bkrivs"; depends=[BiocParallel locfit MultiAssayExperiment plyr S4Vectors]; };
ClassifyR = derive2 { name="ClassifyR"; version="2.2.6"; sha256="1crw7qn6c4h1gx324wgyzjh1z49zb5c43jrl4kiqva8cmds11h46"; depends=[BiocParallel locfit MultiAssayExperiment plyr S4Vectors]; };
Clomial = derive2 { name="Clomial"; version="1.18.1"; sha256="0m1s90syqm6ll61ii1zms1phrycfngl7r2s7d9lxck19imdg8svz"; depends=[matrixStats permute]; };
Clonality = derive2 { name="Clonality"; version="1.30.0"; sha256="0nhlrzy6z8kcfghw3ciy4ymbnmwb7y68bb1ikz7fxi4d5pywzm03"; depends=[DNAcopy]; };
ClusterJudge = derive2 { name="ClusterJudge"; version="1.4.0"; sha256="1yi3hcbk8ka9krrc2q8jv0sq5szpwp3iw3wnn8x9ibn1qyimzwc5"; depends=[httr infotheo jsonlite lattice latticeExtra]; };
ClusterSignificance = derive2 { name="ClusterSignificance"; version="1.10.0"; sha256="1jwl2v9qja11rrdllqkc2hlqiirzcav7s6343d66qaajq02iagzj"; depends=[pracma princurve RColorBrewer scatterplot3d]; };
CoCiteStats = derive2 { name="CoCiteStats"; version="1.54.0"; sha256="0ar66vhlw6zhrrf6bpd82hqwxh4g6apic56mx9xir40302ikc1h4"; depends=[AnnotationDbi org_Hs_eg_db]; };
CoGAPS = derive2 { name="CoGAPS"; version="3.2.2"; sha256="18xkq64kn41v6dk2rnydq9aj1abvc6c5xv2j2xwdl94pc1n6hm3a"; depends=[BH BiocParallel cluster data_table gplots RColorBrewer Rcpp S4Vectors SingleCellExperiment SummarizedExperiment]; };
CoGAPS = derive2 { name="CoGAPS"; version="3.2.40"; sha256="05d8av4q3nvdyf976i9ninb5h3lxk3nr7b327jj7v9qvg9hlmzqh"; depends=[BiocParallel cluster data_table gplots RColorBrewer Rcpp rhdf5 S4Vectors SingleCellExperiment SummarizedExperiment]; };
CoRegNet = derive2 { name="CoRegNet"; version="1.20.0"; sha256="1z8ihzn4i9zzn7cw2376j92cx1b0w543vr9f47xkhnsj871f2v6c"; depends=[arules igraph shiny]; };
CompGO = derive2 { name="CompGO"; version="1.18.0"; sha256="1hzps1isfpdmcxdlpfqhanl0qafydgsgjc5xqxgd8zvib4zb28za"; depends=[GenomicFeatures ggplot2 pathview pcaMethods RDAVIDWebService reshape2 Rgraphviz rtracklayer TxDb_Mmusculus_UCSC_mm9_knownGene]; };
ComplexHeatmap = derive2 { name="ComplexHeatmap"; version="1.20.0"; sha256="0s01dzcfj1lmpqfpsbqw7r4858krfzy499lz4cwx4fq3mbyvy2aj"; depends=[circlize colorspace GetoptLong GlobalOptions RColorBrewer]; };
@ -199,11 +199,11 @@ in with self; {
CrispRVariants = derive2 { name="CrispRVariants"; version="1.10.1"; sha256="0n1mw3ybbdaybbcms12cj4vy21wahq5srny0qnbxjlzyl1zjbpr0"; depends=[AnnotationDbi BiocParallel Biostrings GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 gridExtra IRanges reshape2 Rsamtools S4Vectors]; };
CytoDx = derive2 { name="CytoDx"; version="1.2.1"; sha256="05apvaf4dmkdfsp2aary14i7znjyzk0k6rqcbsk6m98fkp3d9r8b"; depends=[doParallel dplyr flowCore glmnet rpart rpart_plot]; };
CytoML = derive2 { name="CytoML"; version="1.8.1"; sha256="18isg4kjdn975q8vpziisnyxj1jxm4lkq7hi9jy4imf7bffc234i"; depends=[base64enc Biobase data_table flowCore flowUtils flowWorkspace ggcyto graph jsonlite ncdfFlow openCyto plyr RBGL Rgraphviz XML]; };
DAPAR = derive2 { name="DAPAR"; version="1.14.4"; sha256="1qagp6sl4apld3h20sjrbn6pkdr9fx3yznrzlrxgn216hd0b3yjf"; depends=[AnnotationDbi Cairo clusterProfiler cp4p DAPARdata doParallel dplyr factoextra FactoMineR foreach ggplot2 gplots graph highcharter imp4p impute knitr lattice limma lme4 Matrix MSnbase norm openxlsx pcaMethods png preprocessCore RColorBrewer readxl reshape2 scales siggenes stringr tidyr tidyverse tmvtnorm vioplot vsn]; };
DAPAR = derive2 { name="DAPAR"; version="1.14.5"; sha256="0s09y5kpivaichzmfchksaayxchdmqgldcba0waxfxzsapwfb9p1"; depends=[AnnotationDbi Cairo clusterProfiler cp4p DAPARdata doParallel dplyr factoextra FactoMineR foreach ggplot2 gplots graph highcharter imp4p impute knitr lattice limma lme4 Matrix MSnbase norm openxlsx pcaMethods png preprocessCore RColorBrewer readxl reshape2 scales siggenes stringr tidyr tidyverse tmvtnorm vioplot vsn]; };
DART = derive2 { name="DART"; version="1.30.0"; sha256="0dxwy95p43c0shx30y95sj1pl64kqkh2bsnj680q196zgyg937s6"; depends=[igraph]; };
DBChIP = derive2 { name="DBChIP"; version="1.26.0"; sha256="1wk8nvfcfhsymhbi6id0kd1jzcykh6hhikl2040g0v6gi252gv2v"; depends=[DESeq edgeR]; };
DChIPRep = derive2 { name="DChIPRep"; version="1.12.0"; sha256="1avcjr7r54grh3yn5pjbzji3syc8vvah9as7asv3cwmyqzaya4r0"; depends=[assertthat ChIPpeakAnno DESeq2 fdrtool GenomicRanges ggplot2 plyr purrr reshape2 S4Vectors smoothmest soGGi SummarizedExperiment tidyr]; };
DECIPHER = derive2 { name="DECIPHER"; version="2.10.1"; sha256="1qvdlw0had47p2mldahfppwk4c9nqvswqg8qjkg8nvqckb9aka10"; depends=[Biostrings DBI IRanges RSQLite S4Vectors XVector]; };
DECIPHER = derive2 { name="DECIPHER"; version="2.10.2"; sha256="191s87akdjfqdbq4xvz42s10fpq3w7jm6962ndhcibm8kzgz241r"; depends=[Biostrings DBI IRanges RSQLite S4Vectors XVector]; };
DEComplexDisease = derive2 { name="DEComplexDisease"; version="1.2.0"; sha256="1a4m4xs8dd0459vh5bhi96w6vchmqgap3snrj8x6jjlpvkkhwl8l"; depends=[BiocParallel ComplexHeatmap DESeq2 edgeR Rcpp SummarizedExperiment]; };
DEDS = derive2 { name="DEDS"; version="1.56.0"; sha256="1zfgaar3bpss49zhs81mwlfzkx5lv92j8a64xd12ig88is24cw2c"; depends=[]; };
DEFormats = derive2 { name="DEFormats"; version="1.10.1"; sha256="01zhxi2gpbdbfxxh8myq7930rk2zcwdchdj7xa2p4hrl2mzhr7c8"; depends=[checkmate data_table DESeq2 edgeR GenomicRanges S4Vectors SummarizedExperiment]; };
@ -214,14 +214,14 @@ in with self; {
DEScan2 = derive2 { name="DEScan2"; version="1.2.1"; sha256="0l47x2yrxcyj0mfz972acyw2v9n08ib859jb3v9qasrbw04qnvwk"; depends=[BiocGenerics BiocParallel ChIPpeakAnno data_table DelayedArray GenomeInfoDb GenomicAlignments GenomicRanges glue IRanges plyr Rcpp RcppArmadillo rtracklayer S4Vectors SummarizedExperiment]; };
DESeq = derive2 { name="DESeq"; version="1.34.1"; sha256="0bpiixczbhlyaiinpbl6xrpmv72k2bq76bxnw06gl35m4pgs94p2"; depends=[Biobase BiocGenerics genefilter geneplotter lattice locfit MASS RColorBrewer]; };
DESeq2 = derive2 { name="DESeq2"; version="1.22.2"; sha256="0n5ah84mxn87p45drzy0wh2yknmzj1q5i6gv0v9vgg1lj7awb91r"; depends=[Biobase BiocGenerics BiocParallel genefilter geneplotter GenomicRanges ggplot2 Hmisc IRanges locfit Rcpp RcppArmadillo S4Vectors SummarizedExperiment]; };
DEXSeq = derive2 { name="DEXSeq"; version="1.28.1"; sha256="0g5w9bn2nb3m670hkcsnhfvvkza2318z9irlhhwhb3n8rdzlsdym"; depends=[AnnotationDbi Biobase BiocGenerics BiocParallel biomaRt DESeq2 genefilter geneplotter GenomicRanges hwriter IRanges RColorBrewer Rsamtools S4Vectors statmod stringr SummarizedExperiment]; };
DEXSeq = derive2 { name="DEXSeq"; version="1.28.2"; sha256="134znafy7hn38rp4nia4pglz56fz6nbkxrf7z2k1sajfsgxa1hs6"; depends=[AnnotationDbi Biobase BiocGenerics BiocParallel biomaRt DESeq2 genefilter geneplotter GenomicRanges hwriter IRanges RColorBrewer Rsamtools S4Vectors statmod stringr SummarizedExperiment]; };
DEqMS = derive2 { name="DEqMS"; version="1.0.1"; sha256="1869msy07xh9y0yr0mskrkpmzmf4x3vdarvn8wi78hk1scq1zk71"; depends=[ggplot2 limma]; };
DEsingle = derive2 { name="DEsingle"; version="1.2.1"; sha256="0w3b7pz04l60hrbw4k7rkp4xmf8hzxca7pgrjyalf946z6yvky0s"; depends=[bbmle BiocParallel gamlss MASS Matrix maxLik pscl VGAM]; };
DEsubs = derive2 { name="DEsubs"; version="1.8.1"; sha256="0whs5q02lgis04zyf6abd9b5phv3bw508k4ngp197ka02pbpvxxz"; depends=[circlize DESeq DESeq2 EBSeq edgeR ggplot2 graph igraph jsonlite limma locfit Matrix NBPSeq pheatmap RBGL]; };
DFP = derive2 { name="DFP"; version="1.40.0"; sha256="12kb7cjsfdscdwanjbzvwgp1ra0kmijrp1qyx87sxsk4hxk236ml"; depends=[Biobase]; };
DMCHMM = derive2 { name="DMCHMM"; version="1.4.0"; sha256="12jn77dxbcbzbfdsy4l1vycf68bnw2wdhrwnnjc3829arcz2mkph"; depends=[BiocParallel calibrate fdrtool GenomicRanges IRanges multcomp rtracklayer S4Vectors SummarizedExperiment]; };
DMRScan = derive2 { name="DMRScan"; version="1.8.0"; sha256="0vwmkw3abs0v8z49qdkrqxia0kn5i3pl7yqzv42l5xz7d2498s7q"; depends=[GenomeInfoDb GenomicRanges IRanges MASS Matrix mvtnorm RcppRoll]; };
DMRcaller = derive2 { name="DMRcaller"; version="1.14.1"; sha256="17rnqk46ic6y8hz86cl3vfbgqxswmkl04qzgx5xn9npwwbhvp1nv"; depends=[betareg GenomicRanges IRanges Rcpp RcppRoll S4Vectors]; };
DMRcaller = derive2 { name="DMRcaller"; version="1.14.2"; sha256="13x59irimrjff2pa9vw9yw341xm13wxfzhrfv4ylw60jpzbz71i1"; depends=[betareg GenomicRanges IRanges Rcpp RcppRoll S4Vectors]; };
DMRcate = derive2 { name="DMRcate"; version="1.18.0"; sha256="0930rrz2aps91mcqihap9830km9x7if6vgpvjplmacvs1x2k3wyh"; depends=[DMRcatedata DSS GenomicRanges Gviz IRanges limma minfi missMethyl plyr S4Vectors]; };
DMRforPairs = derive2 { name="DMRforPairs"; version="1.18.0"; sha256="11gbnxlkgkx9ynmslxvinfnq39rpg392zbff6g36fd5nsr3dppxd"; depends=[GenomicRanges Gviz R2HTML]; };
DNABarcodes = derive2 { name="DNABarcodes"; version="1.12.0"; sha256="0g6j7ish0fk9jcib94wssjgp1m8ldcp42hyyg1ypr945fa3xghx0"; depends=[BH Matrix Rcpp]; };
@ -242,7 +242,7 @@ in with self; {
DiffLogo = derive2 { name="DiffLogo"; version="2.6.0"; sha256="1an8c2h0vsy8x3q90bgy7gfigz11k460gpi4wlyj6gq8h6bd1fmy"; depends=[cba]; };
Director = derive2 { name="Director"; version="1.8.0"; sha256="0xzds7gi9bp6hp8dpw9c4ls6b1rcfk4w4my1wacf0z9hnwpd60r3"; depends=[htmltools]; };
DirichletMultinomial = derive2 { name="DirichletMultinomial"; version="1.24.1"; sha256="0vazfjzqy78p5g7dnv30lbqbj4bhq4zafd2wh6gdwy2il1fd78xa"; depends=[BiocGenerics IRanges S4Vectors]; };
DominoEffect = derive2 { name="DominoEffect"; version="1.2.0"; sha256="08wrblpsliyshdv8kldr8mwp3zkkr1255120vy780x6b2n6jczsz"; depends=[AnnotationDbi biomaRt Biostrings data_table GenomeInfoDb GenomicRanges IRanges SummarizedExperiment VariantAnnotation]; };
DominoEffect = derive2 { name="DominoEffect"; version="1.2.1"; sha256="0lb3s9lzscnqvs3vq6ah1fib5day98y0fnh1gdjrf49fl8fkgx3r"; depends=[AnnotationDbi biomaRt Biostrings data_table GenomeInfoDb GenomicRanges IRanges SummarizedExperiment VariantAnnotation]; };
Doscheda = derive2 { name="Doscheda"; version="1.4.1"; sha256="01k95cbkwswpnzc53rszsnk55bx6xisdj5i8211h8zgwjsikryik"; depends=[affy calibrate corrgram d3heatmap drc DT ggplot2 gridExtra httr jsonlite limma matrixStats prodlim readxl reshape2 shiny shinydashboard stringr vsn]; };
DriverNet = derive2 { name="DriverNet"; version="1.22.0"; sha256="13yd9inyqkaw363m6apiyclkjpb3f5khbi0vwc90whi8q9wvsl8f"; depends=[]; };
DropletUtils = derive2 { name="DropletUtils"; version="1.2.2"; sha256="0kxfhd7r2r1p0bmzps0d965l84fk63lc1shqywll5rx0scnhlcsw"; depends=[beachmat BiocParallel edgeR HDF5Array Matrix Rcpp rhdf5 Rhdf5lib S4Vectors SingleCellExperiment]; };
@ -264,7 +264,7 @@ in with self; {
EMDomics = derive2 { name="EMDomics"; version="2.12.0"; sha256="1savm8vh1cl8s9rw5jy341a6azx1d8pm0935jvl10ai0cs6q1f22"; depends=[BiocParallel CDFt emdist ggplot2 matrixStats preprocessCore]; };
ENCODExplorer = derive2 { name="ENCODExplorer"; version="2.8.0"; sha256="1836v5yj5rr3mvmsakbz5ccqc0h3dngipigszbrzcb2qb9m55gqf"; depends=[data_table dplyr DT jsonlite RCurl shiny shinythemes stringi stringr tidyr]; };
ENVISIONQuery = derive2 { name="ENVISIONQuery"; version="1.30.0"; sha256="0ciilgg8mw4lzclfqqgfrc6crig15m418qfpcfk9s4ykcnjzzial"; depends=[rJava XML]; };
ENmix = derive2 { name="ENmix"; version="1.18.1"; sha256="0yrpdg6zx9hbrv80j0fbdf7p75qjl678jn7g73q0mlxgx4pg2fxs"; depends=[doParallel foreach geneplotter impute MASS minfi preprocessCore SummarizedExperiment sva wateRmelon]; };
ENmix = derive2 { name="ENmix"; version="1.18.2"; sha256="0fw4bwdi9yax34r50xclzxgjvq2g02ynz9pxyack20xycn3vn3zn"; depends=[doParallel foreach geneplotter impute MASS minfi preprocessCore SummarizedExperiment sva wateRmelon]; };
ERSSA = derive2 { name="ERSSA"; version="1.0.1"; sha256="02g7kp2g3jxk9fy9fv2b1pkzc46067jwzq4p340w9c8ss8hrpqwh"; depends=[BiocParallel DESeq2 edgeR ggplot2 plyr RColorBrewer]; };
EasyqpcR = derive2 { name="EasyqpcR"; version="1.24.0"; sha256="1znawlhb44j21jhspn703d62pi1zknv1khklmsdlspn5db67wpin"; depends=[gWidgetsRGtk2 matrixStats plotrix plyr]; };
EmpiricalBrownsMethod = derive2 { name="EmpiricalBrownsMethod"; version="1.10.0"; sha256="05n0984x77kvxjj80vx4sh7sz2v90wzf4vqsgbkn7wm45ly6x3h0"; depends=[]; };
@ -302,7 +302,7 @@ in with self; {
GDCRNATools = derive2 { name="GDCRNATools"; version="1.2.1"; sha256="0gwf534xkdg9ajlmhaicpl51kyk74hy7inp83nq4l6gr238x0q85"; depends=[BiocParallel biomaRt clusterProfiler DESeq2 DOSE DT edgeR GenomicDataCommons ggplot2 gplots jsonlite limma org_Hs_eg_db pathview rjson shiny survival survminer XML]; };
GDSArray = derive2 { name="GDSArray"; version="1.2.0"; sha256="1yjrdnkbgxdfs5i2s10idy3szc9p6fcq6mv246hbsibl6zxxlqlh"; depends=[BiocGenerics DelayedArray gdsfmt S4Vectors SeqArray SNPRelate]; };
GEM = derive2 { name="GEM"; version="1.8.0"; sha256="008y135dahsrbk2ik5b7hrsjkhg23cxmsfnbyggm000dap6j4a3w"; depends=[ggplot2]; };
GENESIS = derive2 { name="GENESIS"; version="2.12.2"; sha256="00mma6i20z0q0w4vjziqnll6dzdnx3h2rzxrzrhr0ylwy206hyxd"; depends=[Biobase BiocGenerics data_table dplyr foreach gdsfmt GenomicRanges GWASTools igraph IRanges Matrix reshape2 S4Vectors SeqArray SeqVarTools SNPRelate]; };
GENESIS = derive2 { name="GENESIS"; version="2.12.4"; sha256="0ij4cmh01khyqxvv5y5n3h53xhhlm5qj8ijcqqg5mp7byn9nzvvc"; depends=[Biobase BiocGenerics data_table dplyr foreach gdsfmt GenomicRanges GWASTools igraph IRanges Matrix reshape2 S4Vectors SeqArray SeqVarTools SNPRelate]; };
GENIE3 = derive2 { name="GENIE3"; version="1.4.3"; sha256="1wbgfmv2266djrl71cnhgs89ariw9fncf0kbmz3ps6rc4cm0cj77"; depends=[reshape2]; };
GEOmetadb = derive2 { name="GEOmetadb"; version="1.44.0"; sha256="05iwq2qglkc3xdkvc1049m1mzyiw91dmfb41vkqbqkyw7jc4561h"; depends=[GEOquery RSQLite]; };
GEOquery = derive2 { name="GEOquery"; version="2.50.5"; sha256="074dl00c8yi1ihpjkw7vl9vy2hggvipib0jn0hli0wrw7x1h9hg6"; depends=[Biobase dplyr httr limma magrittr readr tidyr xml2]; };
@ -357,10 +357,10 @@ in with self; {
GeneticsPed = derive2 { name="GeneticsPed"; version="1.44.0"; sha256="00v32167gl0kkglrzl3xm5bw7p8mfc933k074mf9lpbbf9s1liy7"; depends=[gdata genetics MASS]; };
GenoGAM = derive2 { name="GenoGAM"; version="2.0.2"; sha256="1vnvsw3jsp9psdd3vlzxvxhsny15j15b3fhyb07fsr26hgd0k5jh"; depends=[BiocParallel Biostrings data_table DelayedArray DESeq2 futile_logger GenomeInfoDb GenomicAlignments GenomicRanges HDF5Array IRanges Matrix Rcpp RcppArmadillo rhdf5 Rsamtools S4Vectors sparseinv SummarizedExperiment]; };
GenomeGraphs = derive2 { name="GenomeGraphs"; version="1.42.0"; sha256="0n3nbhgwnd09fnn7pyaa8n46hhjrz1gkvzbjjf7p9clv6p937y18"; depends=[biomaRt]; };
GenomeInfoDb = derive2 { name="GenomeInfoDb"; version="1.18.1"; sha256="049pyzr8iszv3g7wdqf3pz7vg7bzd450c20ln6fgw4g5xnkkr10s"; depends=[BiocGenerics GenomeInfoDbData IRanges RCurl S4Vectors]; };
GenomeInfoDb = derive2 { name="GenomeInfoDb"; version="1.18.2"; sha256="07bm35jcczpyxap0b3gky4b28z38z423sngzsm19d9krjxr76b5p"; depends=[BiocGenerics GenomeInfoDbData IRanges RCurl S4Vectors]; };
GenomicAlignments = derive2 { name="GenomicAlignments"; version="1.18.1"; sha256="1maslav2r34wjyzh2nlwa862in1ir7i5xk57nw2nlfh5gqy112jd"; depends=[BiocGenerics BiocParallel Biostrings GenomeInfoDb GenomicRanges IRanges Rsamtools S4Vectors SummarizedExperiment]; };
GenomicDataCommons = derive2 { name="GenomicDataCommons"; version="1.6.0"; sha256="00xlskvrcjmj28mqkdi2d4ksqsb603g6wckqvzqyjr417xyyanrl"; depends=[dplyr GenomicRanges httr IRanges jsonlite lazyeval magrittr rappdirs readr S4Vectors SummarizedExperiment xml2]; };
GenomicFeatures = derive2 { name="GenomicFeatures"; version="1.34.3"; sha256="1d9i8fq856hb7bvkldgim4ipzp6v6ax2ki0wgjgxzs1h2q3zpa2v"; depends=[AnnotationDbi Biobase BiocGenerics biomaRt Biostrings DBI GenomeInfoDb GenomicRanges IRanges RCurl RSQLite rtracklayer S4Vectors XVector]; };
GenomicFeatures = derive2 { name="GenomicFeatures"; version="1.34.4"; sha256="09gc1vbqszrr3ixv4hsfan2l18fcf3gg58783mrfwjv6ci9c4w0d"; depends=[AnnotationDbi Biobase BiocGenerics biomaRt Biostrings DBI GenomeInfoDb GenomicRanges IRanges RCurl RSQLite rtracklayer S4Vectors XVector]; };
GenomicFiles = derive2 { name="GenomicFiles"; version="1.18.0"; sha256="0qf2yj4lfnnk64fk125n8sqms01shfqiik04nasx2z3k129ykpxp"; depends=[BiocGenerics BiocParallel GenomeInfoDb GenomicAlignments GenomicRanges IRanges Rsamtools rtracklayer S4Vectors SummarizedExperiment VariantAnnotation]; };
GenomicInteractions = derive2 { name="GenomicInteractions"; version="1.16.0"; sha256="0zy5isp2lqpjm0n0n1gly5bs4izn22yciibyqrnlrr60rmn5s67q"; depends=[Biobase BiocGenerics data_table dplyr GenomeInfoDb GenomicRanges ggplot2 gridExtra Gviz igraph InteractionSet IRanges Rsamtools rtracklayer S4Vectors stringr]; };
GenomicRanges = derive2 { name="GenomicRanges"; version="1.34.0"; sha256="0bgh14d15dpf2iy36qinw45r6n45rqkf0ghazrdl3jfva6vbrb29"; depends=[BiocGenerics GenomeInfoDb IRanges S4Vectors XVector]; };
@ -375,7 +375,7 @@ in with self; {
GraphPAC = derive2 { name="GraphPAC"; version="1.24.0"; sha256="0dwh3xshp74isq3rljlivks04mw4r0vgzg74qwyc2ar5b2j96bbg"; depends=[igraph iPAC RMallow TSP]; };
GreyListChIP = derive2 { name="GreyListChIP"; version="1.14.0"; sha256="1hsjv4r88ldb7pgl5a3im8vdhmbiaj0rrn0clij7jfh5p5r81r1r"; depends=[BSgenome GenomeInfoDb GenomicAlignments GenomicRanges MASS Rsamtools rtracklayer SummarizedExperiment]; };
Guitar = derive2 { name="Guitar"; version="1.20.1"; sha256="1d4j54jdnsi8gi6p0kk6zxkk6kzd1r1k77mw142xlvh8b6zrl3nq"; depends=[GenomicAlignments GenomicFeatures GenomicRanges ggplot2 IRanges Rsamtools rtracklayer]; };
Gviz = derive2 { name="Gviz"; version="1.26.4"; sha256="0jvcivgw0ahv2rjadxmrww76xambhf7silczmh38nn4yn4qw6w9y"; depends=[AnnotationDbi Biobase BiocGenerics biomaRt Biostrings biovizBase BSgenome digest GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges lattice latticeExtra matrixStats RColorBrewer Rsamtools rtracklayer S4Vectors XVector]; };
Gviz = derive2 { name="Gviz"; version="1.26.5"; sha256="1dpkcaar7qgzg3vgafvkplprhwmhzpb7ph009kr6ajm36hx4z81c"; depends=[AnnotationDbi Biobase BiocGenerics biomaRt Biostrings biovizBase BSgenome digest GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges lattice latticeExtra matrixStats RColorBrewer Rsamtools rtracklayer S4Vectors XVector]; };
HDF5Array = derive2 { name="HDF5Array"; version="1.10.1"; sha256="1qwdsygcadl58qj598hfyvs8hp0hqcl9ghnhknahrlhmb7k2bd2d"; depends=[BiocGenerics DelayedArray IRanges rhdf5 S4Vectors]; };
HDTD = derive2 { name="HDTD"; version="1.16.0"; sha256="1girysaq3w4vfmrdb4vx2g0z9f4nb7ly44b72yhvw9fxsdjzbsc5"; depends=[Rcpp RcppArmadillo]; };
HELP = derive2 { name="HELP"; version="1.40.0"; sha256="0l6ysv1wdivimvn895alshz6v6avvp7y2gmdphg4iqrmvmjzsd36"; depends=[Biobase]; };
@ -419,12 +419,12 @@ in with self; {
IdMappingRetrieval = derive2 { name="IdMappingRetrieval"; version="1.30.0"; sha256="1knaavzdvm1iz6crhqhxsxhvlrpa9k6n6d82q21w6qag8lkvwc2x"; depends=[AffyCompatible biomaRt ENVISIONQuery R_methodsS3 R_oo rChoiceDialogs RCurl XML]; };
IdeoViz = derive2 { name="IdeoViz"; version="1.18.0"; sha256="067bd18pb3xyw58xxl0fxa09kcyh4dhdzxbci6i7b82fa17s9hkb"; depends=[Biobase GenomeInfoDb GenomicRanges IRanges RColorBrewer rtracklayer]; };
Imetagene = derive2 { name="Imetagene"; version="1.12.0"; sha256="0lh15nqjxwgjlhhzrrjj9bpbbkxnq2nlgx3v4fik6q4d5rqx0zbb"; depends=[d3heatmap ggplot2 metagene shiny shinyBS shinyFiles shinythemes]; };
ImmuneSpaceR = derive2 { name="ImmuneSpaceR"; version="1.10.2"; sha256="0j0dnvd876xw8pxp43yphzwqyy6avnkf6azf8ihdhdsr7p7dqkn4"; depends=[Biobase curl data_table ggplot2 gplots gtools heatmaply httr pheatmap plotly preprocessCore R6 reshape2 rjson Rlabkey rmarkdown scales]; };
ImmuneSpaceR = derive2 { name="ImmuneSpaceR"; version="1.10.3"; sha256="1d67q276d9nr1fiz9a8lldvggq91sw056slcd8d2pvm55bj4fiwy"; depends=[Biobase curl data_table ggplot2 gplots gtools heatmaply httr pheatmap plotly preprocessCore R6 reshape2 rjson Rlabkey rmarkdown scales]; };
ImpulseDE = derive2 { name="ImpulseDE"; version="1.8.0"; sha256="0jiqclcm0w6nh7j3w5wqv0c6lw0pyn4wczld2fmkqyv71mshmakn"; depends=[amap boot]; };
ImpulseDE2 = derive2 { name="ImpulseDE2"; version="1.6.1"; sha256="0zbrkwaspwaq9aa9il4ahn5lnhbyz8cair5lx354pr1whm3wn8v3"; depends=[Biobase BiocParallel circlize ComplexHeatmap cowplot DESeq2 ggplot2 knitr Matrix S4Vectors SummarizedExperiment]; };
InPAS = derive2 { name="InPAS"; version="1.14.1"; sha256="0r1b5f13yq1nqrfk2ry88m5dnz86pjmf9g158c45jzvw0b9czxyd"; depends=[AnnotationDbi Biobase BiocParallel BSgenome cleanUpdTSeq depmixS4 GenomeInfoDb GenomicFeatures GenomicRanges Gviz IRanges limma preprocessCore S4Vectors seqinr]; };
InTAD = derive2 { name="InTAD"; version="1.2.1"; sha256="0r4qln2cgqab7rpahm94v4321nn4md5yh0479s0px8zbnrmq3cnn"; depends=[Biobase BiocGenerics GenomicRanges ggplot2 ggpubr IRanges mclust MultiAssayExperiment qvalue rtracklayer S4Vectors SummarizedExperiment]; };
IntEREst = derive2 { name="IntEREst"; version="1.6.1"; sha256="0vkrzs96jmkj68pxyi9wm5xxn7p5l8zh86j68pw1857dj0sy8wkr"; depends=[BiocGenerics BiocParallel Biostrings DBI DESeq2 DEXSeq edgeR GenomicAlignments GenomicFeatures GenomicRanges IRanges RMySQL Rsamtools S4Vectors seqinr seqLogo SummarizedExperiment]; };
InTAD = derive2 { name="InTAD"; version="1.2.3"; sha256="1vahq4rh8icka1qqwnqvw3y5hbrss0nnpyll5bvwnm9514sp030w"; depends=[Biobase BiocGenerics GenomicRanges ggplot2 ggpubr IRanges mclust MultiAssayExperiment qvalue rtracklayer S4Vectors SummarizedExperiment]; };
IntEREst = derive2 { name="IntEREst"; version="1.6.2"; sha256="1y9ilxlqi71hy0jzar5bbdn9y9xx7nbfzi6rgkdmf8mpdin5r62f"; depends=[BiocGenerics BiocParallel Biostrings DBI DESeq2 DEXSeq edgeR GenomicAlignments GenomicFeatures GenomicRanges IRanges RMySQL Rsamtools S4Vectors seqinr seqLogo SummarizedExperiment]; };
InterMineR = derive2 { name="InterMineR"; version="1.4.1"; sha256="1v11h22nw3chxkscdmbc9z4186x885lpnh537yyijp9429bab44l"; depends=[Biostrings GenomicRanges httr igraph IRanges RCurl RJSONIO S4Vectors sqldf SummarizedExperiment XML xml2]; };
InteractionSet = derive2 { name="InteractionSet"; version="1.10.0"; sha256="0wirfhmpmkmnmhbqslw4bzvi2msqyqpjy1rrwr5qbd9k5rhx3bzb"; depends=[BiocGenerics GenomeInfoDb GenomicRanges IRanges Matrix Rcpp S4Vectors SummarizedExperiment]; };
IntramiRExploreR = derive2 { name="IntramiRExploreR"; version="1.4.0"; sha256="0cv7g8cca447gvzy13xpx7h5sxg2w9n3pmj74rfqpbcpd1m9h2p4"; depends=[FGNet igraph knitr]; };
@ -453,15 +453,15 @@ in with self; {
Linnorm = derive2 { name="Linnorm"; version="2.6.1"; sha256="1qgk8m5kc409flqxs3vnf228v3z0112q8py9hgfgyiwvi6yzdbp6"; depends=[amap apcluster ellipse fastcluster fpc ggdendro ggplot2 gmodels igraph limma MASS mclust Rcpp RcppArmadillo Rtsne statmod vegan zoo]; };
LiquidAssociation = derive2 { name="LiquidAssociation"; version="1.36.0"; sha256="0hz60m9m0098mqwajw83xkraajlbh4q8617d85mfjcbdgmc483a1"; depends=[Biobase geepack org_Sc_sgd_db yeastCC]; };
Logolas = derive2 { name="Logolas"; version="1.6.0"; sha256="0asi528yb65vwdkxxlsdv9g06fr2y5mzxa3m1669byjb6fjzzs1y"; depends=[Biostrings ggplot2 gridBase LaplacesDemon SQUAREM]; };
LoomExperiment = derive2 { name="LoomExperiment"; version="1.0.2"; sha256="1yknracvm55fqj4ys2z2am6w8q6vr0g52mlkv5ngabss24gzblkk"; depends=[DelayedArray GenomicRanges HDF5Array rhdf5 rtracklayer S4Vectors SingleCellExperiment SummarizedExperiment]; };
LowMACA = derive2 { name="LowMACA"; version="1.12.0"; sha256="027nrw2qypw3iqs4dwr6gn6bhbq8kx6ba3fjvk7cd9lp3pqw580s"; depends=[BiocParallel Biostrings cgdsr data_table httr LowMACAAnnotation motifStack RColorBrewer reshape2 stringr]; };
LoomExperiment = derive2 { name="LoomExperiment"; version="1.0.4"; sha256="18pqixrnln5d60g6a5nay2zw4984bnllqzrpylwx2nrxsindp9n1"; depends=[DelayedArray GenomicRanges HDF5Array rhdf5 rtracklayer S4Vectors SingleCellExperiment SummarizedExperiment]; };
LowMACA = derive2 { name="LowMACA"; version="1.12.1"; sha256="08lh0q88ixad11hgkxs0y1bc7pi3a8f1a70nqxmdwkgghcfziirp"; depends=[BiocParallel Biostrings cgdsr data_table httr LowMACAAnnotation motifStack RColorBrewer reshape2 stringr]; };
LymphoSeq = derive2 { name="LymphoSeq"; version="1.10.0"; sha256="024d13hrw0s0zmza9bd8nm9s79imwajqvzxiaxj5348pj2d212hr"; depends=[Biostrings circlize data_table dplyr ggplot2 ggtree ineq LymphoSeqDB msa phangorn plyr RColorBrewer reshape stringdist UpSetR VennDiagram]; };
M3C = derive2 { name="M3C"; version="1.4.1"; sha256="0l9063bn0sfcq5qxghaj8f98x0pg91fwsd8l64ga8d7pnlm8i5fm"; depends=[cluster dendextend doParallel doSNOW foreach ggplot2 Matrix matrixcalc NMF RColorBrewer Rtsne sigclust survival]; };
M3D = derive2 { name="M3D"; version="1.16.0"; sha256="0a7xs3kqvyxswsa4zcdakij4rvpv1pr4fmplnvxyskhh2zps7xyl"; depends=[BiocGenerics BiSeq GenomicRanges IRanges Rcpp S4Vectors SummarizedExperiment]; };
M3Drop = derive2 { name="M3Drop"; version="1.8.1"; sha256="0bzxv4lnmbz4d7y1c2w7i013rfjscnj1ndb05k9n1i4c9gsknqya"; depends=[bbmle gplots numDeriv RColorBrewer statmod]; };
MACPET = derive2 { name="MACPET"; version="1.2.0"; sha256="0799d3pr5b6g7xbi75pf693768nspdc73qay72naghyql6g91s96"; depends=[BH bigmemory BiocParallel Biostrings futile_logger GenomeInfoDb GenomicAlignments GenomicRanges GEOquery gtools InteractionSet intervals IRanges knitr plyr rbamtools Rbowtie Rcpp Rsamtools rtracklayer S4Vectors ShortRead]; };
MACPET = derive2 { name="MACPET"; version="1.2.0"; sha256="0799d3pr5b6g7xbi75pf693768nspdc73qay72naghyql6g91s96"; depends=[BH bigmemory BiocParallel Biostrings futile_logger GenomeInfoDb GenomicAlignments GenomicRanges GEOquery gtools InteractionSet intervals IRanges knitr plyr Rbowtie Rcpp Rsamtools rtracklayer S4Vectors ShortRead]; };
MADSEQ = derive2 { name="MADSEQ"; version="1.8.0"; sha256="1b7d6niz8lhvd17xjl4hy1yyki049cg6wd3g8wp38bm3zs6dzfd1"; depends=[Biostrings BSgenome BSgenome_Hsapiens_UCSC_hg19 coda GenomeInfoDb GenomicAlignments GenomicRanges IRanges preprocessCore rjags Rsamtools rtracklayer S4Vectors SummarizedExperiment VariantAnnotation vcfR VGAM zlibbioc]; };
MAGeCKFlute = derive2 { name="MAGeCKFlute"; version="1.2.2"; sha256="0jl5k0c0146b5mv34wrn0ld9icgdppvhyqnbx0rk18vgyf81bzjn"; depends=[biomaRt bladderbatch clusterProfiler data_table DOSE ggExtra ggplot2 ggrepel ggsci gridExtra pathview pheatmap png sva]; };
MAGeCKFlute = derive2 { name="MAGeCKFlute"; version="1.2.3"; sha256="1d2lllsz2jdqma1ifdg7xj9fby85az7bifn0h0hj705m6dyla42z"; depends=[biomaRt bladderbatch clusterProfiler data_table DOSE ggExtra ggplot2 ggrepel ggsci gridExtra pathview pheatmap png sva]; };
MAIT = derive2 { name="MAIT"; version="1.16.1"; sha256="0fg3cah81c4gzm3hw590h4grrja2qgfs8mrpkbifrgsclbybnp95"; depends=[agricolae CAMERA caret class e1071 gplots MASS pls plsgenomics Rcpp xcms]; };
MANOR = derive2 { name="MANOR"; version="1.54.0"; sha256="102s71adp93n47sz2hcqs5ihykwcvha6sz7v24p409a7rj8ary38"; depends=[GLAD]; };
MAST = derive2 { name="MAST"; version="1.8.2"; sha256="0rhx655dza0m6yg9jcfz2nmxqahvxx2l91kqgyp7qai0bzz9d9ix"; depends=[abind Biobase BiocGenerics data_table ggplot2 plyr progress reshape2 S4Vectors SingleCellExperiment stringr SummarizedExperiment]; };
@ -495,7 +495,7 @@ in with self; {
MSstats = derive2 { name="MSstats"; version="3.14.1"; sha256="1bgvdq1mfq6rxjf5ag2slrhy4056906wghsirrymf53nw3qz5g6s"; depends=[data_table doSNOW dplyr foreach ggplot2 ggrepel gplots limma lme4 marray MASS minpack_lm preprocessCore randomForest reshape2 snow stringr survival tidyr]; };
MSstatsQC = derive2 { name="MSstatsQC"; version="2.0.1"; sha256="1f6gv1fqm5h6xs91wc1bamyri47qggb872qzriwzvff7ydn0q1ag"; depends=[dplyr ggExtra ggplot2 MSnbase plotly qcmetrics RecordLinkage]; };
MSstatsQCgui = derive2 { name="MSstatsQCgui"; version="1.2.1"; sha256="1k7dhiayf885ax1mg03yg1w4mamk3j1gsm7phszxl3i0j3c2gks7"; depends=[dplyr ggExtra gridExtra MSstatsQC plotly RecordLinkage shiny]; };
MSstatsTMT = derive2 { name="MSstatsTMT"; version="1.0.1"; sha256="0xpxshnqc1ljfhk081185mbchdxr6n5xrlv2zhrzbxi48i3sm5rv"; depends=[data_table dplyr ggplot2 limma lme4 matrixStats MSstats nlme reshape2 tidyr]; };
MSstatsTMT = derive2 { name="MSstatsTMT"; version="1.1.2"; sha256="0aaw3qillcfrjczdmd7s21v551hclnq8fn2zvn91wyr4i82q43rr"; depends=[data_table dplyr ggplot2 limma lme4 matrixStats MSstats nlme reshape2 tidyr]; };
MTseeker = derive2 { name="MTseeker"; version="1.0.6"; sha256="0fsb7k6pkl15q8csygpsjrz4jvy20mfd5rfmhl7q7ffj4d7sprxh"; depends=[Biobase BiocGenerics Biostrings circlize GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges gmapR Homo_sapiens IRanges jsonlite Rsamtools rtracklayer S4Vectors SummarizedExperiment VariantAnnotation VariantTools viridis xml2]; };
MVCClass = derive2 { name="MVCClass"; version="1.56.0"; sha256="1hw36gd1z19dir6fl7j3dzqzi5p1668zbwpcz7l21hbyycv27l0j"; depends=[]; };
MWASTools = derive2 { name="MWASTools"; version="1.6.0"; sha256="0bkl7vgyac6xhjj636vlmynq75zyp6smvjvzg1ymkgg800wylg4c"; depends=[boot car ComplexHeatmap ggplot2 glm2 gridExtra igraph KEGGgraph KEGGREST ppcor qvalue RCurl SummarizedExperiment]; };
@ -533,14 +533,14 @@ in with self; {
MotIV = derive2 { name="MotIV"; version="1.38.0"; sha256="1qrpydwc5bn8f0843qkyhw6920xk8kvq452ird0ij96g6faiv9a8"; depends=[BiocGenerics Biostrings IRanges lattice rGADEM S4Vectors]; };
MotifDb = derive2 { name="MotifDb"; version="1.24.1"; sha256="1q454k3p4ib2z79rcgwyx9s9s7gg5j0vlhca1b579qzi3692m8xi"; depends=[BiocGenerics Biostrings IRanges rtracklayer S4Vectors splitstackshape]; };
Mulcom = derive2 { name="Mulcom"; version="1.32.0"; sha256="0k3illh3dchd5nwa4y87v1n0lkil7p5yiqzg9v65nxv35mhkg0vv"; depends=[Biobase fields]; };
MultiAssayExperiment = derive2 { name="MultiAssayExperiment"; version="1.8.1"; sha256="1lr4mhj15vhhx644i6k91c8cvnam2fam9r7hy480kd0qlc5n54sc"; depends=[Biobase BiocGenerics GenomicRanges IRanges S4Vectors SummarizedExperiment tidyr]; };
MultiAssayExperiment = derive2 { name="MultiAssayExperiment"; version="1.8.3"; sha256="04q1y3gkmf6s6ksd3jvxr0r13gzacrxcdgr1zd3ign0zq2ab5bli"; depends=[Biobase BiocGenerics GenomicRanges IRanges S4Vectors SummarizedExperiment tidyr]; };
MultiDataSet = derive2 { name="MultiDataSet"; version="1.10.0"; sha256="1sr93zdirjqgsffmkv9plaqbg3rfsz8lh96mqv7xrnc3nmhmm65y"; depends=[Biobase BiocGenerics GenomicRanges ggplot2 ggrepel IRanges limma qqman S4Vectors SummarizedExperiment]; };
MultiMed = derive2 { name="MultiMed"; version="2.4.0"; sha256="1dfcqh7px0zzgrg96r3930jxzcgvc91xlfm4q9fnn3w85nzgdnrb"; depends=[]; };
MutationalPatterns = derive2 { name="MutationalPatterns"; version="1.8.0"; sha256="0w9lg1zs106h6rqvy8mhikq6q6q9syw6c1prcxr38ssh85rcih12"; depends=[BiocGenerics Biostrings cowplot GenomeInfoDb GenomicRanges ggdendro ggplot2 IRanges NMF plyr pracma reshape2 S4Vectors SummarizedExperiment VariantAnnotation]; };
NADfinder = derive2 { name="NADfinder"; version="1.6.0"; sha256="01jr6pds2r5h7fmm9z0rajiavx7fh4zxf623s1rdjg9ir6njq5m5"; depends=[ATACseqQC baseline BiocGenerics corrplot csaw EmpiricalBrownsMethod GenomeInfoDb GenomicAlignments GenomicRanges IRanges limma metap rbamtools Rsamtools rtracklayer S4Vectors signal SummarizedExperiment trackViewer]; };
NBSplice = derive2 { name="NBSplice"; version="1.0.1"; sha256="155cyb7h7sn7q6m63cv33wbackdq7ryvnnidcy86321yrfjyx023"; depends=[BiocParallel car edgeR ggplot2 MASS mppa reshape2]; };
NADfinder = derive2 { name="NADfinder"; version="1.6.0"; sha256="01jr6pds2r5h7fmm9z0rajiavx7fh4zxf623s1rdjg9ir6njq5m5"; depends=[ATACseqQC baseline BiocGenerics corrplot csaw EmpiricalBrownsMethod GenomeInfoDb GenomicAlignments GenomicRanges IRanges limma metap Rsamtools rtracklayer S4Vectors signal SummarizedExperiment trackViewer]; };
NBSplice = derive2 { name="NBSplice"; version="1.0.3"; sha256="01ws1v6bks41iw2hbzprwbjx0rf0m10nh1wkfk48qzxzsvlfxn5y"; depends=[BiocParallel car edgeR ggplot2 MASS mppa reshape2]; };
NCIgraph = derive2 { name="NCIgraph"; version="1.30.0"; sha256="16mxxrq6g4szig29cah2a13qp1ybsh8ci37izlq6gpxn0h00maym"; depends=[graph KEGGgraph R_methodsS3 RBGL RCy3]; };
NGScopy = derive2 { name="NGScopy"; version="1.16.1"; sha256="1zfasfbzzay402igag1ynffz2v9ad70wdy5vs02q0api3rkkn406"; depends=[changepoint rbamtools Xmisc]; };
NGScopy = derive2 { name="NGScopy"; version="1.16.1"; sha256="1zfasfbzzay402igag1ynffz2v9ad70wdy5vs02q0api3rkkn406"; depends=[changepoint Xmisc]; };
NOISeq = derive2 { name="NOISeq"; version="2.26.1"; sha256="1wyhhi9ydlbjlz427093mdp5ppby77n37w5c2iyxlpsdk2m2nqsn"; depends=[Biobase Matrix]; };
NTW = derive2 { name="NTW"; version="1.32.0"; sha256="10ndg6mina5wz3w87wpv4mnbxdyj6rhvc9jqf954wmh6gj04vyin"; depends=[mvtnorm]; };
NanoStringDiff = derive2 { name="NanoStringDiff"; version="1.12.0"; sha256="1927ry931ckjrci6yfk3fh774bizh4yb5f7p7x1ra1yxzfizq7k3"; depends=[Biobase matrixStats Rcpp]; };
@ -561,7 +561,7 @@ in with self; {
ORFik = derive2 { name="ORFik"; version="1.2.1"; sha256="0x8pj6j3g8gq3i6fqgnd85s60kadq4shjr4hykf00f9zzkj3gnv9"; depends=[BiocGenerics Biostrings data_table GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges Rcpp Rsamtools rtracklayer S4Vectors]; };
OSAT = derive2 { name="OSAT"; version="1.30.0"; sha256="12cswkscavbkx8cxj0kzk6gz1h8xwp24mwy53dgyr771sch76k7j"; depends=[]; };
OTUbase = derive2 { name="OTUbase"; version="1.32.0"; sha256="0xhwa9yd0qd86j03190riff5z64h93pn7q0b6qb2awwf5zrda8fs"; depends=[Biobase Biostrings IRanges S4Vectors ShortRead vegan]; };
OUTRIDER = derive2 { name="OUTRIDER"; version="1.0.2"; sha256="12y1iwrv9v1kzfj5zqjzkb6h819xn6snbkbxg0j882qsw1mwdhwp"; depends=[BBmisc Biobase BiocGenerics BiocParallel data_table DESeq2 GenomicFeatures GenomicRanges ggplot2 ggpubr gplots IRanges matrixStats pcaMethods plotly plyr PRROC RColorBrewer Rcpp RcppArmadillo reticulate S4Vectors scales SummarizedExperiment]; };
OUTRIDER = derive2 { name="OUTRIDER"; version="1.0.3"; sha256="08zyyybcqa2izj36ckgz6phgqxk4bj56bg1q3sya6j5rdjhbvf7n"; depends=[BBmisc Biobase BiocGenerics BiocParallel data_table DESeq2 GenomicFeatures GenomicRanges ggplot2 ggpubr gplots IRanges matrixStats pcaMethods plotly plyr PRROC RColorBrewer Rcpp RcppArmadillo reticulate S4Vectors scales SummarizedExperiment]; };
OmaDB = derive2 { name="OmaDB"; version="1.2.2"; sha256="16qy6p36mkw4fkyp9yis56zyn88x780767ahnqhnyzqlm9g5kv5w"; depends=[ape Biostrings GenomicRanges httr IRanges jsonlite plyr topGO]; };
OmicCircos = derive2 { name="OmicCircos"; version="1.20.0"; sha256="1akb3djkq0waq1f81zi3nnv8svqf2i8w9agaac732vbdr4cf821d"; depends=[GenomicRanges]; };
OmicsMarkeR = derive2 { name="OmicsMarkeR"; version="1.14.0"; sha256="00a8wwk0z73ipdhjlwkwz4nqpjpyylafds88g8dhz0imk8f24gnj"; depends=[assertive assertive_base caret caTools data_table DiscriMiner e1071 foreach gbm glmnet pamr permute plyr randomForest]; };
@ -573,7 +573,7 @@ in with self; {
OrganismDbi = derive2 { name="OrganismDbi"; version="1.24.0"; sha256="11pyv56cy4iy095h40k6k0mpjdlh6gsb4ld3s57nfa9nd4ypx3yi"; depends=[AnnotationDbi Biobase BiocGenerics BiocManager DBI GenomicFeatures GenomicRanges graph IRanges RBGL S4Vectors]; };
Oscope = derive2 { name="Oscope"; version="1.12.1"; sha256="0dxdif1zw8vw6p8ci1nlgr6pwh6gf27r6c9q1lng79gi6x2ipv75"; depends=[BiocParallel cluster EBSeq testthat]; };
OutlierD = derive2 { name="OutlierD"; version="1.46.0"; sha256="1xbkasaf47qmfqqrm1k3mgnjj63rv30094r0f968q7rxfpdmq90f"; depends=[Biobase quantreg]; };
PAA = derive2 { name="PAA"; version="1.16.0"; sha256="03hd7vvkqfr369wp8r0i9y29li9q91s76wzvbh9scvqd0ngmh9cv"; depends=[e1071 gplots gtools limma MASS randomForest Rcpp ROCR sva]; };
PAA = derive2 { name="PAA"; version="1.16.0"; sha256="03hd7vvkqfr369wp8r0i9y29li9q91s76wzvbh9scvqd0ngmh9cv"; depends=[e1071 gplots gtools limma MASS mRMRe randomForest Rcpp ROCR sva]; };
PADOG = derive2 { name="PADOG"; version="1.24.0"; sha256="0xia09m11j70n2gfmka620pk66vjvzr1376y2lb0g18k5n6k2zxv"; depends=[AnnotationDbi Biobase doRNG foreach GSA hgu133a_db hgu133plus2_db KEGG_db KEGGdzPathwaysGEO limma nlme]; };
PANR = derive2 { name="PANR"; version="1.28.1"; sha256="00ymf82kdgc4pqnmz9hgi9b4pk8cidg8n6icx40rcs5dmlkhl24d"; depends=[igraph MASS pvclust RedeR]; };
PAPi = derive2 { name="PAPi"; version="1.22.1"; sha256="12hv5cf0mc243w7a95hlbgfvll7qs6wcc3vqkpg7k5giy24n8i1q"; depends=[KEGGREST svDialogs]; };
@ -601,7 +601,7 @@ in with self; {
PathoStat = derive2 { name="PathoStat"; version="1.8.4"; sha256="15n8lmv9vgwh1ain21gfgyl5bfnkfs7rnjdjbz69bvy1k2nmgl3y"; 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]; };
PathwaySplice = derive2 { name="PathwaySplice"; version="1.6.1"; sha256="09glsv0hj8yzg79hjjpnfn59w12i7l0n2fpwzg98wiqx7yyza5pk"; depends=[annotate AnnotationDbi AnnotationHub BiasedUrn Biobase BiocGenerics DOSE dplyr EnrichmentBrowser ensembldb gdata geneLenDataBase GO_db goseq gplots gridExtra htmlwidgets igraph JunctionSeq KEGGREST mgcv org_Hs_eg_db org_Mm_eg_db plotly RColorBrewer reshape2 S4Vectors tibble VennDiagram webshot]; };
Pbase = derive2 { name="Pbase"; version="0.22.1"; sha256="0z5g2wbjzzqfw0sjb537j84d4l8bvf8pjav5z39ypzx2inq2zzb5"; depends=[AnnotationFilter Biobase BiocGenerics BiocParallel biomaRt Biostrings cleaver ensembldb GenomicRanges Gviz IRanges MSnbase mzID mzR Pviz Rcpp rtracklayer S4Vectors]; };
PepsNMR = derive2 { name="PepsNMR"; version="1.0.1"; sha256="1i8k4x6s7isfzxsv7mpzq3gsh434d3z373ghvwljgdq7q89bg7h7"; depends=[ggplot2 gridExtra Matrix matrixStats ptw reshape2]; };
PepsNMR = derive2 { name="PepsNMR"; version="1.0.2"; sha256="0x7n8faxrczqwn1kkcp22vwag905pswvr2q198kqbh4fjkxgkmrx"; depends=[ggplot2 gridExtra Matrix matrixStats ptw reshape2]; };
PharmacoGx = derive2 { name="PharmacoGx"; version="1.12.0"; sha256="1ddh6bmrddbdmqdpmyy5mlkqvhrk39c19lzybrirfclq6cydfh5g"; depends=[Biobase caTools downloader lsa magicaxis piano RColorBrewer reshape2]; };
PhenStat = derive2 { name="PhenStat"; version="2.18.0"; sha256="1ilsx9fn0aadw0kly5x4lqs88p8lvwidfi38x3h3gpxpf4gygxzx"; depends=[car corrplot ggplot2 graph knitr lme4 logistf MASS msgps nlme nortest pingr reshape SmoothWin]; };
Pi = derive2 { name="Pi"; version="1.10.0"; sha256="03wzmcz57kdflicjb2wmnxg0fvfmbgizvql5164cf24fsi2lvbgi"; depends=[caret dnet GenomeInfoDb GenomicRanges ggbio ggplot2 ggrepel glmnet Gviz igraph lattice MASS Matrix plot3D randomForest ROCR scales supraHex XGR]; };
@ -609,7 +609,7 @@ in with self; {
Polyfit = derive2 { name="Polyfit"; version="1.16.1"; sha256="0nlclhj5ni09blwf5prpcp2iiflqk17ca3gqjl5shvl9y9v8nbqb"; depends=[DESeq]; };
PowerExplorer = derive2 { name="PowerExplorer"; version="1.2.2"; sha256="14dzv3p79x95w6185r2srnmw1i8n6x2b1fd2chbx42b3xa65xliy"; depends=[Biobase BiocParallel data_table DESeq2 ggplot2 gridExtra MASS ROTS S4Vectors SummarizedExperiment vsn]; };
Prize = derive2 { name="Prize"; version="1.12.1"; sha256="046wvhjqyyc79q88lzcx1jfg73f4sr83japiapzgm5gqnri1hs8r"; depends=[diagram ggplot2 gplots matrixcalc reshape2 stringr]; };
Prostar = derive2 { name="Prostar"; version="1.14.8"; sha256="0i2rz644ji4ys6fb2782kijc9zqf18qzknca3c5qjgbh8p34f7ak"; depends=[BiocManager colourpicker DAPAR DAPARdata data_table DT future highcharter htmlwidgets later promises R_utils rclipboard rhandsontable shiny shinyAce shinyBS shinycssloaders shinyjqui shinyjs shinythemes shinyTree shinyWidgets webshot XML]; };
Prostar = derive2 { name="Prostar"; version="1.14.12"; sha256="0700nkpjmlw7540qms407mm94nsch1jzk8sf30k4qk7fn5rfl1wb"; depends=[BiocManager colourpicker DAPAR DAPARdata data_table DT future highcharter htmlwidgets later promises R_utils rclipboard rhandsontable shiny shinyAce shinyBS shinycssloaders shinyjqui shinyjs shinythemes shinyTree shinyWidgets webshot XML]; };
ProtGenerics = derive2 { name="ProtGenerics"; version="1.14.0"; sha256="053mmxhzncqgigl2iqjlq56qzimlw2zzw31wpzw19rf7rld1vi3b"; depends=[]; };
ProteoMM = derive2 { name="ProteoMM"; version="1.0.1"; sha256="0gyx7pfswxa7p6whyi2d10341vgc9yr3vvi7a2wj1padas9cm0m1"; depends=[biomaRt gdata ggplot2 ggrepel gtools matrixStats]; };
ProteomicsAnnotationHubData = derive2 { name="ProteomicsAnnotationHubData"; version="1.12.0"; sha256="049c0g20kbf12hs3r4il3gpr9chi2w2d2l0s7pkgc1sxyb0aydvs"; depends=[AnnotationHub AnnotationHubData Biobase BiocManager Biostrings GenomeInfoDb MSnbase mzR RCurl]; };
@ -630,7 +630,7 @@ in with self; {
RBioinf = derive2 { name="RBioinf"; version="1.42.0"; sha256="1l2vqnrc6ilsi50zn9f1p174hwc63qhbn05z1ng3d2va3x3qb9hm"; depends=[graph]; };
RCAS = derive2 { name="RCAS"; version="1.8.0"; sha256="0ss5hcg2m7gjji6dd23zxa5bd5a7knwcnada4qs5q2l4clgk39ad"; depends=[AnnotationDbi BiocGenerics biomaRt Biostrings BSgenome_Hsapiens_UCSC_hg19 cowplot data_table DBI DT genomation GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 ggseqlogo knitr motifRG org_Hs_eg_db pbapply pheatmap plotly plotrix proxy rmarkdown RSQLite rtracklayer S4Vectors topGO]; };
RCASPAR = derive2 { name="RCASPAR"; version="1.28.0"; sha256="1d5mr6j7yfv9amdjyyysw79n4yr57ryxybbccc97jbkmqhijp806"; depends=[]; };
RCy3 = derive2 { name="RCy3"; version="2.2.6"; sha256="09wsqpzkpxjjdfsy7w9mcrmrw1cva46fbjz42rswsfqrf87xq6mp"; depends=[BiocGenerics graph httr igraph R_utils RJSONIO XML]; };
RCy3 = derive2 { name="RCy3"; version="2.2.9"; sha256="04n73hgh2brfrl9rqmiq1afg7hpvq0l6zbl2h1yqzrgmxgzrx0cv"; depends=[BiocGenerics graph httr igraph R_utils RJSONIO XML]; };
RCyjs = derive2 { name="RCyjs"; version="2.4.0"; sha256="1m5zxa5r9kjcfacgv8ny6pa2a5xd94kajmb054074r7av4ymig5z"; depends=[base64enc BiocGenerics BrowserViz graph httpuv]; };
RDAVIDWebService = derive2 { name="RDAVIDWebService"; version="1.20.0"; sha256="0agdz7r7qcrxmvcm3d6zs36p239ldhc01qa4c4b4dxvlsq5gh6wk"; depends=[Category ggplot2 GO_db GOstats graph RBGL rJava]; };
RDRToolbox = derive2 { name="RDRToolbox"; version="1.32.0"; sha256="01dpaniy2chd7kim6q9lqq65pfs3y1z05jrhgjmrmc7hg0yp1zb1"; depends=[MASS rgl]; };
@ -685,7 +685,7 @@ in with self; {
Rchemcpp = derive2 { name="Rchemcpp"; version="2.20.1"; sha256="00sb9xaj51vna030c6nkb27r3ymj98a27kl97ksa86di3a8n4162"; depends=[ChemmineR Rcpp]; };
RchyOptimyx = derive2 { name="RchyOptimyx"; version="2.22.0"; sha256="10kk9h1cknpdgbmn5k7aabrfr60n66i5yjxbj81x7ji6yk1ramcg"; depends=[flowType graph Rgraphviz sfsmisc]; };
RcisTarget = derive2 { name="RcisTarget"; version="1.2.1"; sha256="0ggwhfm5yl68qapbr3sxz206mpc8vqi9g4x3isxvrcf94q9jb7iq"; depends=[AUCell BiocGenerics data_table feather GSEABase R_utils SummarizedExperiment]; };
Rcpi = derive2 { name="Rcpi"; version="1.18.1"; sha256="1fr6wr1w7xyxmqhpmgwcvfxf0m43gxqpfnrpkm35rya2lkk4994h"; depends=[Biostrings ChemmineR doParallel fmcsR foreach GOSemSim rcdk RCurl rjson]; };
Rcpi = derive2 { name="Rcpi"; version="1.18.2"; sha256="0kd61ajb4lm5b974476204kw9pkavi2l2n7m6zynblpdccpp913f"; depends=[Biostrings ChemmineR doParallel fmcsR foreach GOSemSim rcdk RCurl rjson]; };
Rdisop = derive2 { name="Rdisop"; version="1.42.1"; sha256="0pir401z19wx433sxr2r01a5ckd4myygyv0jxj4wfq1fkfpmi1kl"; depends=[Rcpp RcppClassic]; };
ReQON = derive2 { name="ReQON"; version="1.28.0"; sha256="1llklca4bz2plkmwgvpw7xrn8hxh1vnf6sk91z1yzld49w1b6rxc"; depends=[rJava Rsamtools seqbias]; };
ReactomePA = derive2 { name="ReactomePA"; version="1.26.0"; sha256="1kglvgn1sjnx9rm45lxp0ji19vzb8qlvjs01agsdbvkn19im5nkm"; depends=[AnnotationDbi DOSE enrichplot ggplot2 ggraph graphite igraph reactome_db]; };
@ -698,13 +698,13 @@ in with self; {
Rgin = derive2 { name="Rgin"; version="1.2.0"; sha256="0jj8asqp7p45rlag34m0x2lasw6mdj4rdi4ywnm5bk2cim50pji6"; depends=[RcppEigen]; };
Rgraphviz = derive2 { name="Rgraphviz"; version="2.26.0"; sha256="0bp6517xsih0wng2rgkh9z4r1afqhwl3h04z6ssm7p4cdj0ahm4y"; depends=[graph]; };
Rhdf5lib = derive2 { name="Rhdf5lib"; version="1.4.2"; sha256="06bxd3wz8lrvh2hzvmjpdv4lvzj5lz9353bw5b3zb98cb8w9r2j5"; depends=[]; };
Rhtslib = derive2 { name="Rhtslib"; version="1.14.0"; sha256="1h4q54f8za3aaxgy186zf2165sar5c3cgxkk44lq5hzx5pxkl5wn"; depends=[zlibbioc]; };
Rhtslib = derive2 { name="Rhtslib"; version="1.14.1"; sha256="13fv78sk5g0gqfl3ks3rps3zc1k66a4lzxvgn36r7ix43yxk7hnr"; depends=[zlibbioc]; };
RiboProfiling = derive2 { name="RiboProfiling"; version="1.12.0"; sha256="1njvkd1khmf3rbp3dkz5z63wp79z4wmk4kzd3p3amky3w5by070z"; depends=[BiocGenerics Biostrings data_table GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggbio ggplot2 IRanges plyr reshape2 Rsamtools rtracklayer S4Vectors sqldf]; };
Ringo = derive2 { name="Ringo"; version="1.46.0"; sha256="1zg8sq4hqq3yldghfs1m2jn15qmdk6i1pr7c3aq73a6k99qyzihd"; depends=[Biobase BiocGenerics genefilter lattice limma Matrix RColorBrewer vsn]; };
Risa = derive2 { name="Risa"; version="1.24.0"; sha256="1ln68rxv7wx96b3p2fh70jva07j9hj1cfflxyw34i32qkp2840hm"; depends=[affy Biobase biocViews Rcpp xcms]; };
Rmagpie = derive2 { name="Rmagpie"; version="1.38.0"; sha256="0di8vf3cj7y2srydjq74r7gmksqhjh3r8wmffq1k96knd68nx0sx"; depends=[Biobase e1071 kernlab pamr]; };
RmiR = derive2 { name="RmiR"; version="1.38.0"; sha256="0gv6cm5mh54xh2n25mpy6ak849rcppnajq04y7nw9hjv1i66g125"; depends=[DBI RmiR_Hs_miRNA RSVGTipsDevice]; };
Rmmquant = derive2 { name="Rmmquant"; version="1.0.2"; sha256="0v4gx4zdpfl5gh1z9m9z1gjkl749zga7w210s284c1fyhnpn4anp"; depends=[BiocStyle DESeq2 devtools GenomicRanges org_Mm_eg_db Rcpp S4Vectors SummarizedExperiment TBX20BamSubset TxDb_Mmusculus_UCSC_mm9_knownGene]; };
Rmmquant = derive2 { name="Rmmquant"; version="1.0.4"; sha256="085yn4qg5sn7cbl7gj3b56n7mxiagdj4k8zqqd131dsd5kzwlylc"; depends=[BiocStyle DESeq2 devtools GenomicRanges org_Mm_eg_db Rcpp S4Vectors SummarizedExperiment TBX20BamSubset TxDb_Mmusculus_UCSC_mm9_knownGene]; };
RnBeads = derive2 { name="RnBeads"; version="2.0.1"; sha256="0lfvl0k138dhniffb4c8wdicsihajr6rnrfmmmcgxk2wh6ciibi5"; depends=[BiocGenerics cluster ff fields GenomicRanges ggplot2 gplots gridExtra illuminaio IRanges limma MASS matrixStats methylumi plyr S4Vectors]; };
RnaSeqSampleSize = derive2 { name="RnaSeqSampleSize"; version="1.14.1"; sha256="1gxsp3nr5ww3xlqyac704lczsa5xxyz748lpfpkghj4mi3h0lwa8"; depends=[biomaRt edgeR heatmap3 KEGGREST matlab Rcpp RnaSeqSampleSizeData]; };
Rnits = derive2 { name="Rnits"; version="1.16.0"; sha256="1l96jvyq0afkv2k3gasf0420wbhrs1nv1f5xx0h9f4mhcx81hr7q"; depends=[affy Biobase boot ggplot2 impute limma qvalue reshape2]; };
@ -712,7 +712,7 @@ in with self; {
RpsiXML = derive2 { name="RpsiXML"; version="2.24.0"; sha256="1l9p5mi7b78cwh4pvwqwxx15rr4hms11m5r0vp0d2krfp7ih9m8h"; depends=[annotate AnnotationDbi Biobase graph hypergraph RBGL XML]; };
Rqc = derive2 { name="Rqc"; version="1.16.2"; sha256="1cxa6c9k9ahcji2c979hr0xz9hv7m8w4l6aiczfdhcnjraa4k2qq"; depends=[BiocGenerics BiocParallel BiocStyle Biostrings biovizBase digest GenomicAlignments GenomicFiles ggplot2 IRanges knitr markdown plyr Rcpp reshape2 Rsamtools S4Vectors shiny ShortRead]; };
Rsamtools = derive2 { name="Rsamtools"; version="1.34.1"; sha256="02paq7klabdkaf1b8pmmbpmyqsj3yncnfsz62rgka6r4dpsilwk9"; depends=[BiocGenerics BiocParallel Biostrings bitops GenomeInfoDb GenomicRanges IRanges S4Vectors XVector zlibbioc]; };
Rsubread = derive2 { name="Rsubread"; version="1.32.2"; sha256="1kpishka8m9vp0zjmpmmg4g37s0iw8i01sa4zvwd9py18lc1arzd"; depends=[]; };
Rsubread = derive2 { name="Rsubread"; version="1.32.4"; sha256="1d0gc3pa7zjz2sa4689xxzppikv7xd6k1d8f1x7h973cyiq5iaj3"; depends=[]; };
Rtreemix = derive2 { name="Rtreemix"; version="1.44.0"; sha256="013x6rdxsxynr8s0x8a1nk7xcanvgkm2lid9bip3v240bg9wwha4"; depends=[Biobase graph Hmisc]; };
S4Vectors = derive2 { name="S4Vectors"; version="0.20.1"; sha256="18whrw67nxn82xshckl2pjy7d14sa3c27h3n9naqyqwz88lr6dzg"; depends=[BiocGenerics]; };
SAGx = derive2 { name="SAGx"; version="1.56.0"; sha256="0p81jfm7fr907npbl1qrl4yswbz2a2pgmng5ww68xwmkayxkns79"; depends=[Biobase multtest]; };
@ -721,7 +721,7 @@ in with self; {
SC3 = derive2 { name="SC3"; version="1.10.1"; sha256="04hqbw8k3f2nki5c9brkjlqm072cyw1ppgwlr7id3xqmg4w38l6w"; depends=[BiocGenerics cluster doParallel doRNG e1071 foreach ggplot2 pheatmap Rcpp RcppArmadillo robustbase ROCR rrcov S4Vectors shiny SingleCellExperiment SummarizedExperiment WriteXLS]; };
SCAN_UPC = derive2 { name="SCAN.UPC"; version="2.24.1"; sha256="00sfnc9pdw8j7gbrc6z4v9ji8kwndabr8zxw8agkbf2zz8pmq4jx"; depends=[affy affyio Biobase Biostrings foreach GEOquery IRanges MASS oligo sva]; };
SCBN = derive2 { name="SCBN"; version="1.0.0"; sha256="0cfmpwpp9drz13rrrwg030db1jprxfw2nkxlwlwscaj1vb4q69fv"; depends=[]; };
SCnorm = derive2 { name="SCnorm"; version="1.4.5"; sha256="0gplv7l91bskx75vn4ihy8a0m9v64ny3jhshdx2xaiq0sw4nm1s1"; depends=[BiocParallel cluster data_table forcats ggplot2 moments quantreg S4Vectors SingleCellExperiment SummarizedExperiment]; };
SCnorm = derive2 { name="SCnorm"; version="1.4.7"; sha256="1jlfxwqy1gm1v0a40dd3p5zicr0wa4m7k4nqnf5ypbkngf31zfv9"; depends=[BiocParallel cluster data_table forcats ggplot2 moments quantreg S4Vectors SingleCellExperiment SummarizedExperiment]; };
SDAMS = derive2 { name="SDAMS"; version="1.2.1"; sha256="0cr1mazrbq4hc2gql7bj4pvqd1vdzvpmg6r3dhvybb4prpdl25ys"; depends=[qvalue SummarizedExperiment trust]; };
SELEX = derive2 { name="SELEX"; version="1.14.0"; sha256="1hcsngnxv4q0ig80nr91x1qlxi2swcx9xlvayng25izzjc6yj1k8"; depends=[Biostrings rJava]; };
SEPA = derive2 { name="SEPA"; version="1.12.0"; sha256="04dl578fm1zdd30q9d5dxhcm1xvkn19ijda07yxdsxifik4297fp"; depends=[ggplot2 org_Hs_eg_db org_Mm_eg_db reshape2 segmented shiny topGO]; };
@ -763,10 +763,10 @@ in with self; {
Scale4C = derive2 { name="Scale4C"; version="1.4.0"; sha256="12d8l6j57gwnrigzyprfw03rzgsni7n75ws2hi1ldybx7bx3nlag"; depends=[GenomicRanges IRanges smoothie SummarizedExperiment]; };
Sconify = derive2 { name="Sconify"; version="1.2.1"; sha256="141iq9k1psyc25vf1i8hh52i3dckas1l928yjr59p25qng0z4hfy"; depends=[dplyr flowCore FNN ggplot2 magrittr readr Rtsne tibble]; };
SemDist = derive2 { name="SemDist"; version="1.16.0"; sha256="086lparkzxssz78dn67x4f7c3pw45y7gj2ldvhmkfqyynfm57giq"; depends=[annotate AnnotationDbi GO_db]; };
SeqArray = derive2 { name="SeqArray"; version="1.22.3"; sha256="0014pgklkjkrl7k15fln02gwa2k3z7kaaaq7jc7xjpc35s5bbikd"; depends=[Biostrings gdsfmt GenomeInfoDb GenomicRanges IRanges S4Vectors]; };
SeqArray = derive2 { name="SeqArray"; version="1.22.5"; sha256="1fm1r4s7bxckzzd2309j0fa4q3k5bk2ghzwff697kawi5cxb0fhh"; depends=[Biostrings gdsfmt GenomeInfoDb GenomicRanges IRanges S4Vectors]; };
SeqGSEA = derive2 { name="SeqGSEA"; version="1.22.1"; sha256="1c4lfs9bfdmbq732c13fvph5gwp6ac0fxa489al9lghwxnbkjpqf"; depends=[Biobase biomaRt DESeq doParallel]; };
SeqSQC = derive2 { name="SeqSQC"; version="1.4.0"; sha256="1dg4dm45s7l5dgq2cr6g9a5a65jlpf801z3a1x42h36ybgs7gg3j"; depends=[e1071 ExperimentHub gdsfmt GenomicRanges GGally ggplot2 IRanges rbokeh RColorBrewer reshape2 rmarkdown S4Vectors SNPRelate]; };
SeqVarTools = derive2 { name="SeqVarTools"; version="1.20.1"; sha256="0rfpbasz30r51kqbgmy1l99famly9ynzaq4nbdd13fsz0dqwj2xw"; depends=[Biobase dplyr gdsfmt GenomicRanges GWASExactHW IRanges logistf Matrix rlang S4Vectors SeqArray tidyr]; };
SeqVarTools = derive2 { name="SeqVarTools"; version="1.20.2"; sha256="03z40cmymq6agbmp061kvk4xm4cgilb3gyls5ymwyn4p56m0ks2a"; depends=[Biobase dplyr gdsfmt GenomicRanges GWASExactHW IRanges logistf Matrix rlang S4Vectors SeqArray tidyr]; };
ShortRead = derive2 { name="ShortRead"; version="1.40.0"; sha256="0iks123i1adkb9i2q4wvfqdmmj9dy867jvngj9757y8gj6xbcpy1"; depends=[Biobase BiocGenerics BiocParallel Biostrings GenomeInfoDb GenomicAlignments GenomicRanges hwriter IRanges lattice latticeExtra Rsamtools S4Vectors XVector zlibbioc]; };
SigCheck = derive2 { name="SigCheck"; version="2.14.0"; sha256="0k00lrzpjfdcp3yvjbd1bc3710pa0dd884k4yyq43nv0cv9f4szp"; depends=[Biobase BiocParallel e1071 MLInterfaces survival]; };
SigFuge = derive2 { name="SigFuge"; version="1.20.0"; sha256="0z78yg43wklzrpqawpprgb6nm1wngkd97g09aa9nzv91p05k85dp"; depends=[GenomicRanges ggplot2 matlab reshape sigclust]; };
@ -780,16 +780,16 @@ in with self; {
SplicingGraphs = derive2 { name="SplicingGraphs"; version="1.22.2"; sha256="19isf8wxy7lpaqr4zy5319sx9r2bm6mh8djgcbabg6ns198iy0kq"; depends=[BiocGenerics BiocParallel GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges graph igraph IRanges Rgraphviz Rsamtools S4Vectors]; };
StarBioTrek = derive2 { name="StarBioTrek"; version="1.8.1"; sha256="0lhad99k077sknbvlyd1hpgn4swgkq9lg76dxq7hs1aj1lamqx8d"; depends=[AnnotationDbi e1071 igraph KEGGREST org_Hs_eg_db ROCR SpidermiR]; };
Starr = derive2 { name="Starr"; version="1.38.0"; sha256="1rrs366d8yr02077v34l6yr8w361s94zira2gcf935kkmfrclgij"; depends=[affxparser affy MASS pspline Ringo zlibbioc]; };
Streamer = derive2 { name="Streamer"; version="1.28.0"; sha256="163rhpr042dk5ch47yrgfjsa5hnbhbz4jcnisvlcmmp0jd12qsrr"; depends=[BiocGenerics graph RBGL]; };
Streamer = derive2 { name="Streamer"; version="1.28.1"; sha256="0spqdjmfz1iaa6rcmbzn9d8z60cs1k0smvnnsdjlg7frdh039ra8"; depends=[BiocGenerics graph RBGL]; };
SummarizedBenchmark = derive2 { name="SummarizedBenchmark"; version="2.0.1"; sha256="18gmzwxjwg8j63z213x8r0j6jpmgx4yca29495c2hp4r9gv6hbzr"; depends=[BiocGenerics BiocParallel crayon digest dplyr ggplot2 mclust rlang S4Vectors sessioninfo stringr SummarizedExperiment tibble tidyr UpSetR]; };
SummarizedExperiment = derive2 { name="SummarizedExperiment"; version="1.12.0"; sha256="07805572xhpj5mfwq6kw1ha21wgalqvhh4ydvafyl1bnf3r20vps"; depends=[Biobase BiocGenerics DelayedArray GenomeInfoDb GenomicRanges IRanges Matrix S4Vectors]; };
Sushi = derive2 { name="Sushi"; version="1.20.0"; sha256="0dv5di0hgbvk9cxnqhyf18mdjl50k6bk00a89r6zgp83rbxwr1r8"; depends=[biomaRt zoo]; };
SwathXtend = derive2 { name="SwathXtend"; version="2.4.0"; sha256="0986srxbi3f7pfnhghh9dznwrl9k5qrcmcf1vqa3lg06bwz7pbsc"; depends=[e1071 lattice openxlsx VennDiagram]; };
SwimR = derive2 { name="SwimR"; version="1.20.0"; sha256="0sgci3rs4kak79yibcvxw3mjb30y9q8hacqykrpav2sjyqc6fcy1"; depends=[gplots heatmap_plus R2HTML signal]; };
TCC = derive2 { name="TCC"; version="1.22.1"; sha256="0yfjlr5pgdnkrcv97cqhkm5xdn7dlspbf3fd60ai8zm2iw62x031"; depends=[baySeq DESeq DESeq2 edgeR ROC]; };
TCGAbiolinks = derive2 { name="TCGAbiolinks"; version="2.10.3"; sha256="0kc3sw83mq07wglgdkfchvzm2hp7pw8qfaj9zp7jbiivzxj15bc2"; depends=[biomaRt circlize ComplexHeatmap ConsensusClusterPlus data_table doParallel downloader dplyr EDASeq edgeR genefilter GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 ggrepel ggthemes gridExtra httr IRanges jsonlite knitr limma matlab plyr R_utils RColorBrewer readr rvest S4Vectors scales selectr stringr SummarizedExperiment survival survminer sva tibble tidyr XML xml2]; };
TCGAbiolinksGUI = derive2 { name="TCGAbiolinksGUI"; version="1.8.0"; sha256="1af30xy7yk9hqwc4gcr02nprgxgn2ivq6cb2jigzabhi2bjmm70q"; depends=[caret clusterProfiler colourpicker data_table downloader DT ELMER ggplot2 ggrepel IlluminaHumanMethylation27kanno_ilmn12_hg19 IlluminaHumanMethylation27kmanifest IlluminaHumanMethylation450kanno_ilmn12_hg19 IlluminaHumanMethylation450kmanifest IlluminaHumanMethylationEPICanno_ilm10b2_hg19 IlluminaHumanMethylationEPICmanifest maftools minfi pathview plotly readr shiny shinyBS shinydashboard shinyFiles shinyjs stringr SummarizedExperiment TCGAbiolinks TCGAbiolinksGUI_data]; };
TCGAutils = derive2 { name="TCGAutils"; version="1.2.1"; sha256="1ilvh59qz6bp6pgvcyj51xgmf2kiz416211h8xn8z4kvim5dvpra"; depends=[AnnotationDbi BiocGenerics GenomeInfoDb GenomicDataCommons GenomicFeatures GenomicRanges IRanges MultiAssayExperiment RaggedExperiment rvest S4Vectors stringr SummarizedExperiment xml2]; };
TCGAbiolinks = derive2 { name="TCGAbiolinks"; version="2.10.4"; sha256="04h3s4gxjpb8pgw7mcmw3mlbdmcxpvb4lc643snvg6z7j3asmykv"; depends=[biomaRt circlize ComplexHeatmap ConsensusClusterPlus data_table doParallel downloader dplyr EDASeq edgeR genefilter GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 ggrepel ggthemes gridExtra httr IRanges jsonlite knitr limma matlab plyr R_utils RColorBrewer readr rvest S4Vectors scales selectr sesame stringr SummarizedExperiment survival survminer sva tibble tidyr XML xml2]; };
TCGAbiolinksGUI = derive2 { name="TCGAbiolinksGUI"; version="1.8.1"; sha256="1bj4pvchg0fj6gifbkg79fi314ssl8zp4rylp2ib0jfliqjx5199"; depends=[caret clusterProfiler colourpicker data_table downloader DT ELMER ggplot2 ggrepel maftools pathview plotly readr sesame sesameData shiny shinyBS shinydashboard shinyFiles shinyjs stringr SummarizedExperiment TCGAbiolinks TCGAbiolinksGUI_data]; };
TCGAutils = derive2 { name="TCGAutils"; version="1.2.2"; sha256="00wi93lxq06aczjj9g5drs4jy6c4md550hbqxf6p11f07mh7kqcy"; depends=[AnnotationDbi BiocGenerics GenomeInfoDb GenomicDataCommons GenomicFeatures GenomicRanges IRanges MultiAssayExperiment RaggedExperiment rvest S4Vectors stringr SummarizedExperiment xml2]; };
TCseq = derive2 { name="TCseq"; version="1.6.1"; sha256="01lakq59skdivgyb613x4rwxfap9iiccwi2ixd0nl7vw97wsjfc3"; depends=[BiocGenerics cluster e1071 edgeR GenomicAlignments GenomicRanges ggplot2 IRanges locfit reshape2 Rsamtools SummarizedExperiment]; };
TDARACNE = derive2 { name="TDARACNE"; version="1.32.0"; sha256="0b7p7pl9sn2g3f7wv405nwng2xknxqhdwqm2bkr4czxcrmwdal5f"; depends=[Biobase GenKern Rgraphviz]; };
TEQC = derive2 { name="TEQC"; version="4.4.0"; sha256="16aj8nadcpnv1lqqz7pfss7vc2s5h0k79ahxb4l4405j8yrf16hl"; depends=[Biobase BiocGenerics hwriter IRanges Rsamtools]; };
@ -809,7 +809,7 @@ in with self; {
TVTB = derive2 { name="TVTB"; version="1.8.0"; sha256="058h38x6x69jsp8qsdy7mz9wjjvhw4dwbph14qgqvagbaiaj7v19"; depends=[AnnotationFilter BiocGenerics BiocParallel Biostrings ensembldb ensemblVEP GenomeInfoDb GenomicRanges GGally ggplot2 Gviz IRanges limma reshape2 Rsamtools S4Vectors SummarizedExperiment VariantAnnotation]; };
TarSeqQC = derive2 { name="TarSeqQC"; version="1.12.0"; sha256="1p1fwmkikh6a6sff3hmdxc3z4ypxz2iv1j544gfmsq47pibn8cgp"; depends=[BiocGenerics BiocParallel Biostrings cowplot GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 Hmisc IRanges openxlsx plyr reshape2 Rsamtools S4Vectors]; };
TargetScore = derive2 { name="TargetScore"; version="1.20.0"; sha256="0kxiv5rghq3fw416gg3z7gfram146hjaf5pjd5hbyvy7rydilvbz"; depends=[Matrix pracma]; };
TargetSearch = derive2 { name="TargetSearch"; version="1.38.1"; sha256="0gk91i4g5ly6y2xzs8h8f90w3pm6mp3habjjy2bv60jsqxpi3pcb"; depends=[ncdf4]; };
TargetSearch = derive2 { name="TargetSearch"; version="1.38.2"; sha256="1vad4kxsanmjk78wjqq6lq3mjif01b89f09mhg0rwp902bdqlk35"; depends=[ncdf4]; };
TimeSeriesExperiment = derive2 { name="TimeSeriesExperiment"; version="1.0.4"; sha256="03ny8w0z29jblph8nsysrqm7l2m2qpij52415vv1an4wpv821pgd"; depends=[DESeq2 dplyr dynamicTreeCut edgeR ggplot2 Hmisc limma magrittr proxy S4Vectors SummarizedExperiment tibble tidyr vegan viridis]; };
TissueEnrich = derive2 { name="TissueEnrich"; version="1.2.1"; sha256="13nbcrj441wrbjn8xbrb8fn802bimhnaxjb980bn55l0ix7npy1c"; depends=[dplyr ensurer ggplot2 GSEABase SummarizedExperiment tidyr]; };
TitanCNA = derive2 { name="TitanCNA"; version="1.20.1"; sha256="0vp5i30n3f8kschal06i3v4szl1vl3lvry522csxdax3pram90g8"; depends=[data_table dplyr foreach GenomeInfoDb GenomicRanges IRanges Rsamtools VariantAnnotation]; };
@ -818,14 +818,14 @@ in with self; {
TransView = derive2 { name="TransView"; version="1.26.1"; sha256="1y2cdyg0hixm3zxasib18ql9917vnf43cjn9wpkx52fqfwa62ly3"; depends=[BiocGenerics GenomicRanges gplots IRanges Rsamtools S4Vectors zlibbioc]; };
Trendy = derive2 { name="Trendy"; version="1.4.4"; sha256="0vmm2gvg3yb5chqj4fg5l0x86zm19vj5zcj32nzgba6c1s38qxhb"; depends=[BiocParallel DT gplots magrittr S4Vectors segmented shiny shinyFiles SummarizedExperiment]; };
TurboNorm = derive2 { name="TurboNorm"; version="1.30.0"; sha256="0a3f1zgj914rklrdilcnqfcr4g3mhg1bzfzxr6nn2cqin47hlakp"; depends=[affy convert lattice limma marray]; };
TxRegInfra = derive2 { name="TxRegInfra"; version="1.2.0"; sha256="03bf4bk1gwiy3bqlihczy3fg5vw66nkfi1gg6s6szy2hh8jrd2js"; depends=[BiocParallel GenomeInfoDb GenomicRanges IRanges mongolite RaggedExperiment rjson S4Vectors SummarizedExperiment]; };
TxRegInfra = derive2 { name="TxRegInfra"; version="1.2.1"; sha256="1qvc0lb3x3s1hv1qw1yih79kdd7pa5wa9wdd94yd8z4vfasmfvav"; depends=[BiocParallel GenomeInfoDb GenomicRanges IRanges mongolite RaggedExperiment rjson S4Vectors SummarizedExperiment]; };
TypeInfo = derive2 { name="TypeInfo"; version="1.48.0"; sha256="0h2jnshr2sgyay3isiapfagjjh4wnff7nw711j4gxw9wg328w24l"; depends=[]; };
UNDO = derive2 { name="UNDO"; version="1.24.0"; sha256="0yins1aw7gfp5qxmsai4l59nl5i6diq1h2frvdshsg6dbfxkzy67"; depends=[Biobase BiocGenerics boot MASS nnls]; };
Ularcirc = derive2 { name="Ularcirc"; version="1.0.0"; sha256="1h4pv78x78wlgq0zmdjgdapjp7bxzdkw078pq9h6xzhkwvmyilz3"; depends=[AnnotationHub Biostrings BSgenome data_table DT GenomeInfoDb GenomeInfoDbData GenomicFeatures gsubfn httpuv mirbase_db moments shiny shinyFiles Sushi yaml]; };
UniProt_ws = derive2 { name="UniProt.ws"; version="2.22.0"; sha256="02rb0ygc3pikb8qbi8134n9hjzza4n3bvqbqfl5dqb2n1ibkknmq"; depends=[AnnotationDbi BiocFileCache BiocGenerics rappdirs RCurl RSQLite]; };
Uniquorn = derive2 { name="Uniquorn"; version="2.2.1"; sha256="0wh57344icpd84l4gj7lz2n75mhpw6ywsir7zj4ky83p30x066sr"; depends=[data_table doParallel foreach GenomicRanges IRanges R_utils stringr VariantAnnotation WriteXLS]; };
VanillaICE = derive2 { name="VanillaICE"; version="1.44.0"; sha256="0v4bqcwbbzabmq1pcs55j3jlhqssr2jsr9hxh76p1n7d6fw4dgs6"; depends=[Biobase BiocGenerics BSgenome_Hsapiens_UCSC_hg18 crlmm data_table foreach GenomeInfoDb GenomicRanges IRanges lattice matrixStats oligoClasses S4Vectors SummarizedExperiment]; };
VariantAnnotation = derive2 { name="VariantAnnotation"; version="1.28.10"; sha256="0kxf583cgkdz1shi85r0mpnfxmzi7s5f6srd1czbdl2iibvrm8jn"; depends=[AnnotationDbi Biobase BiocGenerics Biostrings BSgenome DBI GenomeInfoDb GenomicFeatures GenomicRanges IRanges Rsamtools rtracklayer S4Vectors SummarizedExperiment XVector zlibbioc]; };
VariantAnnotation = derive2 { name="VariantAnnotation"; version="1.28.11"; sha256="19bxi5b9fzqdjadb8bfm8xsgi6nvrwbgn1xcpk59bnmv9vzjkwrh"; depends=[AnnotationDbi Biobase BiocGenerics Biostrings BSgenome DBI GenomeInfoDb GenomicFeatures GenomicRanges IRanges Rsamtools rtracklayer S4Vectors SummarizedExperiment XVector zlibbioc]; };
VariantFiltering = derive2 { name="VariantFiltering"; version="1.18.0"; sha256="13z1x1v9xbdzsfn9x66b6sd18pla98cwd5zvxkwaiph8rp8bgvic"; 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]; };
VariantTools = derive2 { name="VariantTools"; version="1.24.0"; sha256="1ml3pl7xnxvzr6zkypr80xzw6nffswk29gzxycn42473sc4ixn7j"; depends=[Biobase BiocGenerics BiocParallel Biostrings BSgenome GenomeInfoDb GenomicFeatures GenomicRanges IRanges Matrix Rsamtools rtracklayer S4Vectors VariantAnnotation]; };
Vega = derive2 { name="Vega"; version="1.30.0"; sha256="035f2ly3y5i4cirwvfham5kpyawg9scfvfvyn7ys4lyjxx59y4dd"; depends=[]; };
@ -868,7 +868,7 @@ in with self; {
anamiR = derive2 { name="anamiR"; version="1.10.0"; sha256="0yk56vkibnbfwlnixh5r4a9iw9pnmavl7lv4p0jdmv2wnx85gzgz"; depends=[agricolae DBI DESeq2 gage gplots limma lumi RMySQL S4Vectors SummarizedExperiment]; };
annaffy = derive2 { name="annaffy"; version="1.54.0"; sha256="16c6allp4vlx0g3nffanrm0mkkf8s2n31dccw4bflnx2pr81bmd5"; depends=[AnnotationDbi Biobase DBI GO_db KEGG_db]; };
annmap = derive2 { name="annmap"; version="1.24.0"; sha256="12047l7sc3ayvicqnlxc424kbvbiiz1nn4rczd1n50b8kzc25fjs"; depends=[Biobase BiocGenerics DBI digest genefilter GenomicRanges IRanges lattice RMySQL Rsamtools]; };
annotate = derive2 { name="annotate"; version="1.60.0"; sha256="0p6c96lay23a67dyirgnwzm2yw22m592z780vy6p4nqwla8ha18n"; depends=[AnnotationDbi Biobase BiocGenerics DBI RCurl XML xtable]; };
annotate = derive2 { name="annotate"; version="1.60.1"; sha256="0pk6ayr3vyqxk850ljkbyil4i382ngfqcbxlv0qrp62yfqgzcjwp"; depends=[AnnotationDbi Biobase BiocGenerics DBI RCurl XML xtable]; };
annotationTools = derive2 { name="annotationTools"; version="1.56.0"; sha256="0hqy0mq6pkn05p2dv4pw24p697yvikhdn351adf2ynldy6f3sl9z"; depends=[Biobase]; };
annotatr = derive2 { name="annotatr"; version="1.8.0"; sha256="1rknhlndn9fxa68dbkqjphiv50xqp28vf1259k5w7vlm75vvdkdv"; depends=[AnnotationDbi AnnotationHub dplyr GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 IRanges readr regioneR reshape2 rtracklayer S4Vectors]; };
anota = derive2 { name="anota"; version="1.30.0"; sha256="182fp6dpws516y0igvwn6936higfqvy25haa0xs273f8aczr9cf0"; depends=[multtest qvalue]; };
@ -881,7 +881,7 @@ in with self; {
arrayMvout = derive2 { name="arrayMvout"; version="1.40.0"; sha256="1m3n2pqm40wsq7x7acspcq268608pnx58mndqfcbv813685b70p5"; depends=[affy affyContam Biobase lumi mdqc parody simpleaffy]; };
arrayQuality = derive2 { name="arrayQuality"; version="1.60.0"; sha256="0fbvlilz111ahlm50gmwwjydpasbplr0lpj3dz9apawi0jff4f4a"; depends=[gridBase hexbin limma marray RColorBrewer]; };
arrayQualityMetrics = derive2 { name="arrayQualityMetrics"; version="3.38.0"; sha256="0xhzz9ixc5mp49cwpi4smdgdc3mrf1ppzhx8dpjahq1f7r3xnbb5"; depends=[affy affyPLM beadarray Biobase Cairo genefilter gridSVG Hmisc hwriter lattice latticeExtra limma RColorBrewer setRNG vsn XML]; };
artMS = derive2 { name="artMS"; version="1.0.6"; sha256="1dxjg7ykfw2w0a2cvpvfsp54g7kr8lib8fjncnzvwzcgi417y3xf"; depends=[AnnotationDbi biomaRt bit64 circlize cluster ComplexHeatmap corrplot data_table dplyr factoextra FactoMineR getopt ggdendro ggplot2 ggrepel gplots gProfileR limma MSstats openxlsx org_Hs_eg_db org_Mm_eg_db PerformanceAnalytics pheatmap plotly plyr RColorBrewer reshape2 seqinr stringr tidyr UpSetR VennDiagram yaml]; };
artMS = derive2 { name="artMS"; version="1.0.10"; sha256="02ma6nsvr0yh8dwwwv29xxv1qm3lyglwagrzxzlys7kdz0crwvsd"; depends=[AnnotationDbi biomaRt bit64 circlize cluster ComplexHeatmap corrplot data_table dplyr factoextra FactoMineR getopt ggdendro ggplot2 ggrepel gplots gProfileR limma MSstats openxlsx org_Hs_eg_db org_Mm_eg_db PerformanceAnalytics pheatmap plotly plyr RColorBrewer reshape2 seqinr stringr tidyr UpSetR VennDiagram yaml]; };
attract = derive2 { name="attract"; version="1.34.1"; sha256="1370w8qvmiv8r48hk29mlh53xs5a78qpz6pbax7fq7q9xip7fbs0"; depends=[AnnotationDbi Biobase cluster GOstats KEGGREST limma org_Hs_eg_db reactome_db]; };
bacon = derive2 { name="bacon"; version="1.10.1"; sha256="1pd3p1cfggiy08458vplsy3s1zm5jqqcwrv4fks8ra2kf97j38df"; depends=[BiocParallel ellipse ggplot2]; };
ballgown = derive2 { name="ballgown"; version="2.14.1"; sha256="073jyv98s05cxx8n83c20chh0k1sbw8rndldcdfq3habahllf8si"; depends=[Biobase GenomeInfoDb GenomicRanges IRanges limma RColorBrewer rtracklayer S4Vectors sva]; };
@ -898,7 +898,7 @@ in with self; {
bgx = derive2 { name="bgx"; version="1.48.1"; sha256="0ygqbqpbrp4hy5dp4g7nn7zrfar855a7bp16dxcv7646vp3yrzk4"; depends=[affy Biobase gcrma Rcpp]; };
bigmelon = derive2 { name="bigmelon"; version="1.8.0"; sha256="1wc5n5cq05a7qv0b46ywbgg1fbz0s8hyf83g861dxw8jhhmnm717"; depends=[Biobase BiocGenerics gdsfmt GEOquery methylumi minfi wateRmelon]; };
bigmemoryExtras = derive2 { name="bigmemoryExtras"; version="1.30.0"; sha256="0pzqchv9namv73nm2vr6wjny7ghja8bs73s7xp4ixyfg4d1i9h06"; depends=[bigmemory]; };
bioCancer = derive2 { name="bioCancer"; version="1.10.0"; sha256="17f72vs9h66ny9z0n4fbp6533phrdv60a7ck386rfvpgafdrqh7s"; depends=[AlgDesign AnnotationFuncs Biobase cgdsr clusterProfiler DiagrammeR DOSE dplyr DT geNetClassifier htmlwidgets org_Hs_eg_db plyr r_import radiant_data reactome_db ReactomePA shiny shinythemes tibble visNetwork XML]; };
bioCancer = derive2 { name="bioCancer"; version="1.10.1"; sha256="0qqigpnq082fr45xg50a0z2s474m65zhd8qkpv3ini0gq8ydq80l"; depends=[AlgDesign AnnotationFuncs Biobase cgdsr clusterProfiler DiagrammeR DOSE dplyr DT geNetClassifier htmlwidgets org_Hs_eg_db plyr r_import radiant_data reactome_db ReactomePA shiny shinythemes tibble visNetwork XML]; };
bioDist = derive2 { name="bioDist"; version="1.54.0"; sha256="1pl6z8yx1pns19y924x79ky4vqx180hifvy7n4mdhv6mjvhjkijl"; depends=[Biobase KernSmooth]; };
bioassayR = derive2 { name="bioassayR"; version="1.20.1"; sha256="1zf1ykmn3wq6jxb6k1v00qna5wjlh4yy7x35x2k6zqgn7df4607z"; depends=[BiocGenerics ChemmineR DBI Matrix rjson RSQLite XML]; };
biobroom = derive2 { name="biobroom"; version="1.14.0"; sha256="1xfqa666n8h65y277a1g56r1z76x9fn0dnj45cqgx3ddaz0v1nil"; depends=[Biobase broom dplyr tidyr]; };
@ -923,11 +923,11 @@ in with self; {
bumphunter = derive2 { name="bumphunter"; version="1.24.5"; sha256="1f9vk3srffbx8jpza40nd18a4y0p0z8q40mx55dlcnddkwrqi19b"; depends=[AnnotationDbi BiocGenerics doRNG foreach GenomeInfoDb GenomicFeatures GenomicRanges IRanges iterators limma locfit matrixStats S4Vectors]; };
cTRAP = derive2 { name="cTRAP"; version="1.0.3"; sha256="14rfnqmp2mgnkyhgyvlplv4alnwm909pw586n7nc53r82ph4m0f0"; depends=[cowplot data_table fgsea ggplot2 httr limma pbapply piano plyr R_utils readr rhdf5]; };
caOmicsV = derive2 { name="caOmicsV"; version="1.12.1"; sha256="1nqa1f5dbx11lfripaz2l7pkymcgi5vbiglhhk0kz4n0p5p1pjz3"; depends=[bc3net igraph]; };
canceR = derive2 { name="canceR"; version="1.16.0"; sha256="0kfhvkjc6mssp6jphac4p1f2sjc8j08apiwznj621w3wxa2gnkby"; depends=[Biobase cgdsr circlize Formula geNetClassifier GSEABase GSEAlm phenoTest plyr rpart RUnit survival tcltk2 tkrplot]; };
canceR = derive2 { name="canceR"; version="1.16.01"; sha256="1ddjs8fvjkn8w59p1q3lxpn8s7pcd557f8dnbj6nm6zcpbyp6bll"; depends=[Biobase cgdsr circlize Formula geNetClassifier GSEABase GSEAlm phenoTest plyr rpart RUnit survival tcltk2 tkrplot]; };
cancerclass = derive2 { name="cancerclass"; version="1.26.0"; sha256="1fsfxi95iyb2bhy64xdja4231bfs9byzzvdpsf6abd8myqaflcpx"; depends=[binom Biobase]; };
casper = derive2 { name="casper"; version="2.16.1"; sha256="1wr7l1lri00g3fxafhjkj82y3nlh488x9ayjf4x3bcyv20d0lc2a"; depends=[Biobase BiocGenerics coda EBarrays gaga GenomeInfoDb GenomicFeatures GenomicRanges gtools IRanges limma mgcv Rsamtools rtracklayer S4Vectors sqldf survival VGAM]; };
categoryCompare = derive2 { name="categoryCompare"; version="1.26.0"; sha256="1kb4b833wn5qf3d6vic0jf0p0h6dhgcpjnxnqd6b4bhva0y3jcfd"; depends=[annotate AnnotationDbi Biobase BiocGenerics Category colorspace GOstats graph GSEABase hwriter RCy3]; };
cbaf = derive2 { name="cbaf"; version="1.4.0"; sha256="10rcph5kk1kdd1idl7wvh766qfg25462sc0airwcsm2w6xw7xgqf"; depends=[BiocFileCache cgdsr genefilter gplots RColorBrewer xlsx]; };
cbaf = derive2 { name="cbaf"; version="1.4.1"; sha256="04qspghxibf05fjx8sbqq8kxhx0y0lh8v5mv4lzzy13bhms9nfsk"; depends=[BiocFileCache cgdsr genefilter gplots RColorBrewer xlsx]; };
ccfindR = derive2 { name="ccfindR"; version="1.2.1"; sha256="0gcbqjlb4jpxw2rswwgld5nazzzsphh8kdaqpjhn96qslkfxqlrw"; depends=[ape gtools irlba Matrix RColorBrewer Rcpp RcppEigen Rmpi Rtsne S4Vectors SingleCellExperiment SummarizedExperiment]; };
ccmap = derive2 { name="ccmap"; version="1.8.0"; sha256="1vkkm455nhhg123jwl2kv3gdf3mvw5zab4whym0vh33rm499hrks"; depends=[AnnotationDbi BiocManager ccdata data_table doParallel foreach lsa xgboost]; };
ccrepe = derive2 { name="ccrepe"; version="1.18.1"; sha256="10c6mypr2q3j420bvldl59h1y58i8l06piwqr1ji80z6r6xk96vx"; depends=[infotheo]; };
@ -951,7 +951,7 @@ in with self; {
chromVAR = derive2 { name="chromVAR"; version="1.4.1"; sha256="16q9pmjlaqc7nvaxg9arfsrrnpcyzvz0gb5zq7l3g2jgjp4pfi30"; depends=[BiocGenerics BiocParallel Biostrings BSgenome DT GenomeInfoDb GenomicRanges ggplot2 IRanges Matrix miniUI nabor plotly RColorBrewer Rcpp RcppArmadillo Rsamtools Rtsne S4Vectors shiny SummarizedExperiment TFBSTools]; };
chromstaR = derive2 { name="chromstaR"; version="1.8.1"; sha256="0ad8q80r7c2bh4a4qy0n82n0ln6fpwwmabcicpdqlvaiahdnp9ph"; depends=[bamsignals chromstaRData doParallel foreach GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 IRanges mvtnorm reshape2 Rsamtools S4Vectors]; };
chromswitch = derive2 { name="chromswitch"; version="1.4.1"; sha256="12c9p8val2hfz41kcgph0ms2vfb8dvh754c5z70kyy4wg9n4d28s"; depends=[Biobase BiocParallel cluster dplyr GenomicRanges gplots IRanges lazyeval magrittr matrixStats NMF rtracklayer S4Vectors tidyr]; };
cicero = derive2 { name="cicero"; version="1.0.14"; sha256="0n4dl6d5fp989y86lnnhjdlmqcy7qyr5ayb1dp2q05rpa7qkv8cf"; depends=[assertthat Biobase BiocGenerics data_table dplyr FNN GenomicRanges ggplot2 glasso Gviz igraph IRanges Matrix monocle plyr reshape2 S4Vectors stringr tibble VGAM]; };
cicero = derive2 { name="cicero"; version="1.0.15"; sha256="0awxl47rk6f15x8qb70azjs80fsfd8c78bvr4hgc3dmiyik5frs2"; depends=[assertthat Biobase BiocGenerics data_table dplyr FNN GenomicRanges ggplot2 glasso Gviz igraph IRanges Matrix monocle plyr reshape2 S4Vectors stringr tibble VGAM]; };
cisPath = derive2 { name="cisPath"; version="1.22.0"; sha256="07ym4ma35vngdbv8fdqf755kiafgrn02bizn77pfkzvrf7xsz5c7"; depends=[]; };
cleanUpdTSeq = derive2 { name="cleanUpdTSeq"; version="1.20.0"; sha256="0lmdrx332p43xw1y3bnq7abr6589rwyirn3kljkzjy8j86v0bgbi"; depends=[BiocGenerics BSgenome BSgenome_Drerio_UCSC_danRer7 e1071 GenomicRanges seqinr]; };
cleaver = derive2 { name="cleaver"; version="1.20.0"; sha256="0b00a5n87hcssnra9j0qfsq260a83g9p35rnhpg8ywv3kk6z85cc"; depends=[Biostrings IRanges S4Vectors]; };
@ -979,7 +979,7 @@ in with self; {
compartmap = derive2 { name="compartmap"; version="1.0.3"; sha256="0p7ww7wgfnnankkjlq9jgqqcw9l9k0k2ynzmgxdqsyndpi9ghmgr"; depends=[GenomicRanges gtools Homo_sapiens minfi mixOmics SummarizedExperiment]; };
compcodeR = derive2 { name="compcodeR"; version="1.18.1"; sha256="0833zar5zpgns3rlr6nsfagd1ypp62c2779kzajvsrjm61406mrs"; depends=[caTools edgeR gdata ggplot2 gplots gtools KernSmooth knitr lattice limma markdown MASS modeest ROCR sm stringr vioplot]; };
condcomp = derive2 { name="condcomp"; version="1.0.1"; sha256="1drp9zicf29alh8cq093ns7asl67zhb12mbi0cjd3n1z4i19919j"; depends=[cluster ggplot2 ggrepel outliers]; };
consensus = derive2 { name="consensus"; version="1.0.2"; sha256="1z07qrdpm6nf3xpv7g7km6vxmx5glvyc0zgianns9r75cc8fnnw9"; depends=[gplots matrixStats RColorBrewer]; };
consensus = derive2 { name="consensus"; version="1.0.3"; sha256="0lylnis33dbnd6vxp3g4pvn1cvzslpy6j2y1j31bw5an1i5lg4l2"; depends=[gplots matrixStats RColorBrewer]; };
consensusDE = derive2 { name="consensusDE"; version="1.0.6"; sha256="1wakskzc6bcq0a8inacsd062z5sgaqkk8317pa2jdn8kyfqxgq9z"; depends=[airway AnnotationDbi Biobase BiocGenerics BiocParallel Biostrings dendextend DESeq2 EDASeq edgeR GenomicAlignments GenomicFeatures limma pcaMethods RColorBrewer Rsamtools RUVSeq S4Vectors SummarizedExperiment TxDb_Dmelanogaster_UCSC_dm3_ensGene]; };
consensusOV = derive2 { name="consensusOV"; version="1.4.1"; sha256="0bqqbk2mcj1q5bpyv5gykxpjf3c1gszm5irbdhp1hnkvpy5rxdyw"; depends=[Biobase gdata genefu GSVA limma matrixStats randomForest]; };
consensusSeekeR = derive2 { name="consensusSeekeR"; version="1.10.0"; sha256="1rww42z71x6d7ckjdm6xa4cvvqazbwghq6na3srq5aarp6pyh34w"; depends=[BiocGenerics BiocParallel GenomeInfoDb GenomicRanges IRanges rtracklayer S4Vectors stringr]; };
@ -1025,13 +1025,13 @@ in with self; {
diffGeneAnalysis = derive2 { name="diffGeneAnalysis"; version="1.64.0"; sha256="00f088phbix7wrcjrpf3n2a2ps102sbc85f4fg5sqwdw6bvchk9c"; depends=[minpack_lm]; };
diffHic = derive2 { name="diffHic"; version="1.14.0"; sha256="1yjsvwwai9jflg743nyksj7krm0f2pdy2y2rwnmd3cpwh73yy6al"; depends=[BiocGenerics Biostrings BSgenome csaw edgeR GenomeInfoDb GenomicRanges InteractionSet IRanges limma locfit Rcpp rhdf5 Rhtslib Rsamtools rtracklayer S4Vectors SummarizedExperiment zlibbioc]; };
diffcoexp = derive2 { name="diffcoexp"; version="1.2.0"; sha256="1kkm0mw7q81yls750ky9rvx0n9iljgq8j5p9h08yxpr46jc3j8k0"; depends=[BiocGenerics DiffCorr igraph psych SummarizedExperiment WGCNA]; };
diffcyt = derive2 { name="diffcyt"; version="1.2.8"; sha256="169b6dn6hkx95xklfkhyiblwkrlpzrd4ag660q6kq7a4aii6n202"; depends=[circlize ComplexHeatmap dplyr edgeR flowCore FlowSOM limma lme4 magrittr multcomp reshape2 S4Vectors SummarizedExperiment tidyr]; };
diffcyt = derive2 { name="diffcyt"; version="1.2.10"; sha256="1sfq2irrhc7g8nx74x0qf74zp5nbb1fmhf047fcwm9yf5y0y3cam"; depends=[circlize ComplexHeatmap dplyr edgeR flowCore FlowSOM limma lme4 magrittr multcomp reshape2 S4Vectors SummarizedExperiment tidyr]; };
diffloop = derive2 { name="diffloop"; version="1.10.0"; sha256="0fi1vvzfifhdgcnal1axn69dqbgpjqsicjgqw6gj41db50zi1fi6"; depends=[Biobase biomaRt data_table dplyr edgeR foreach GenomeInfoDb GenomicRanges ggplot2 IRanges limma locfit matrixStats pbapply plyr readr reshape2 rtracklayer S4Vectors statmod Sushi]; };
diffuStats = derive2 { name="diffuStats"; version="1.2.0"; sha256="1hg8scxhndgp0r4m5r7rjliirb4371g9d3lqx2h9mgshadwz5h0r"; depends=[expm igraph MASS Matrix plyr precrec Rcpp RcppArmadillo RcppParallel]; };
diggit = derive2 { name="diggit"; version="1.14.0"; sha256="1kpi1ahwc90mpfwmy6rsf4argf7fss99lr2v0s99aj39m3lwd2dw"; depends=[Biobase ks viper]; };
discordant = derive2 { name="discordant"; version="1.6.1"; sha256="12zh1qm7l7zq310y4n5fimia1jkxm3ia81br0illyna0kx10b9wq"; depends=[Biobase biwt gtools MASS]; };
dks = derive2 { name="dks"; version="1.28.0"; sha256="0md8x07f117clhxmmrqaki5g5y8r13c4yrw8vk6yvcsf9prybdah"; depends=[cubature]; };
dmrseq = derive2 { name="dmrseq"; version="1.2.2"; sha256="0vmnka9p6kk9q5rbi5kzxvazvzw0k2fkby7ql4rczyfx4prr7bz6"; depends=[AnnotationHub annotatr BiocParallel bsseq bumphunter DelayedMatrixStats GenomeInfoDb GenomicRanges ggplot2 IRanges locfit matrixStats nlme outliers RColorBrewer rtracklayer S4Vectors]; };
dmrseq = derive2 { name="dmrseq"; version="1.2.3"; sha256="1dy5r96cffwml8g0r40nibz4qjy1x5m64z2ncwi728zp2fxg1hwh"; depends=[AnnotationHub annotatr BiocParallel bsseq bumphunter DelayedMatrixStats GenomeInfoDb GenomicRanges ggplot2 IRanges locfit matrixStats nlme outliers RColorBrewer rtracklayer S4Vectors]; };
doppelgangR = derive2 { name="doppelgangR"; version="1.10.1"; sha256="14jlrvx6xb6h8x9qg0fm0hb11dk906ja8vfl1wn6wgdrh8fw6brl"; depends=[Biobase BiocParallel digest impute mnormt SummarizedExperiment sva]; };
drawProteins = derive2 { name="drawProteins"; version="1.2.0"; sha256="13zqpghzpqg92i4mlfmvwx1l1mb7swqmyhisqjp546jzs7vixv25"; depends=[dplyr ggplot2 httr readr stringr]; };
dualKS = derive2 { name="dualKS"; version="1.42.0"; sha256="0mn0mjzncd53wq0jwq2gfcj3mcsfl81hgsaxnf1dqjwqnw4jy1y3"; depends=[affy Biobase]; };
@ -1046,7 +1046,7 @@ in with self; {
eisa = derive2 { name="eisa"; version="1.34.0"; sha256="1717bpmrr1kmd1a8rqlarhqcrk786vjw55shn5sd8c89f25vspdx"; depends=[AnnotationDbi Biobase BiocGenerics Category DBI genefilter isa2]; };
enrichplot = derive2 { name="enrichplot"; version="1.2.0"; sha256="0cxqfpy6py4k3z3lnlkiwx89r4ymfpdc4hm25dfpazqgjflz5is7"; depends=[AnnotationDbi cowplot DOSE europepmc ggplot2 ggplotify ggraph ggridges GOSemSim gridExtra igraph purrr RColorBrewer reshape2 UpSetR]; };
ensemblVEP = derive2 { name="ensemblVEP"; version="1.24.0"; sha256="148phm407clbhp87snazan120bh5hcl90xgbhlwyz0a36i4kjfvc"; depends=[BiocGenerics Biostrings GenomeInfoDb GenomicRanges S4Vectors SummarizedExperiment VariantAnnotation]; };
ensembldb = derive2 { name="ensembldb"; version="2.6.5"; sha256="19pf66bh3z3hgdzbwwbzi0xbwhkrn1avrsw19kzpxdvp7q0xn9as"; depends=[AnnotationDbi AnnotationFilter Biobase BiocGenerics Biostrings curl DBI GenomeInfoDb GenomicFeatures GenomicRanges IRanges ProtGenerics Rsamtools RSQLite rtracklayer S4Vectors]; };
ensembldb = derive2 { name="ensembldb"; version="2.6.7"; sha256="1wqq0m1fgvgkzq5zr2s9cj2s7qkg9lx3dwwsqixzs5fn52p4dn7f"; depends=[AnnotationDbi AnnotationFilter Biobase BiocGenerics Biostrings curl DBI GenomeInfoDb GenomicFeatures GenomicRanges IRanges ProtGenerics Rsamtools RSQLite rtracklayer S4Vectors]; };
epiNEM = derive2 { name="epiNEM"; version="1.6.0"; sha256="1pzcajgqsm6mvw8i7aav0918856ghndrdp93831s6zmdkgxzpw2v"; depends=[BoolNet e1071 graph gtools igraph lattice latticeExtra minet nem pcalg RColorBrewer]; };
epigenomix = derive2 { name="epigenomix"; version="1.22.0"; sha256="0cyf35fygr3rgkcfqhb9p9xgl1lydqprzhn3m189yqm3xqck41il"; depends=[beadarray Biobase BiocGenerics GenomeInfoDb GenomicRanges IRanges MCMCpack Rsamtools S4Vectors SummarizedExperiment]; };
epivizr = derive2 { name="epivizr"; version="2.12.0"; sha256="0ms29c5vl0nn8p4v1l5falmwc8xb6wa8fjbfwrgpz8dphidp7mnm"; depends=[epivizrData epivizrServer GenomicRanges IRanges S4Vectors]; };
@ -1056,7 +1056,7 @@ in with self; {
epivizrStandalone = derive2 { name="epivizrStandalone"; version="1.10.0"; sha256="0jvx2kc0wqq7rzi1a3lv94i33cgcqhdpny4563kgjcz9g3qaggsd"; depends=[BiocGenerics epivizr epivizrServer GenomeInfoDb GenomicFeatures git2r S4Vectors]; };
erccdashboard = derive2 { name="erccdashboard"; version="1.16.1"; sha256="0xf5nfzjp0jbhyvcia0bxj8rwcmd033gxgvrwrlcq2535v27sdz9"; depends=[edgeR ggplot2 gplots gridExtra gtools limma locfit MASS plyr qvalue reshape2 ROCR scales stringr]; };
erma = derive2 { name="erma"; version="0.14.0"; sha256="0hj9iz904rr1y66442lkxjywkw1ydyxxlhmjirawbf09ic5ad4g9"; depends=[AnnotationDbi Biobase BiocGenerics BiocParallel GenomeInfoDb GenomicFiles GenomicRanges ggplot2 Homo_sapiens IRanges rtracklayer S4Vectors shiny SummarizedExperiment]; };
esATAC = derive2 { name="esATAC"; version="1.4.2"; sha256="0ahqpab9n07fj5jzhj4jilc01a19b8xs70f7q9w91j9bwsjc6rp4"; depends=[AnnotationDbi BiocGenerics BiocManager Biostrings BSgenome ChIPseeker clusterProfiler corrplot DiagrammeR digest GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 igraph IRanges JASPAR2016 knitr magrittr motifmatchr R_utils Rbowtie2 Rcpp rJava rmarkdown Rsamtools rtracklayer S4Vectors ShortRead TFBSTools VennDiagram]; };
esATAC = derive2 { name="esATAC"; version="1.4.4"; sha256="1azw914d18ny7qw8305gqly3cczr9kr2d0wgnb9fk2kl5zp7pkhm"; depends=[AnnotationDbi BiocGenerics BiocManager Biostrings BSgenome ChIPseeker clusterProfiler corrplot DiagrammeR digest GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 igraph IRanges JASPAR2016 knitr magrittr motifmatchr R_utils Rbowtie2 Rcpp rJava rmarkdown Rsamtools rtracklayer S4Vectors ShortRead TFBSTools VennDiagram]; };
esetVis = derive2 { name="esetVis"; version="1.8.0"; sha256="0n2b7qkgy0gh9jfxi5mgsr8g41141435maq1yniw9mqa3hddwjjp"; depends=[Biobase hexbin MASS MLP mpm Rtsne]; };
eudysbiome = derive2 { name="eudysbiome"; version="1.12.0"; sha256="09lhzfhlmrw6f50c6d21lmyfh3k4hwrg6waiv1qjg6iavhnbc2a0"; depends=[Biostrings plyr R_utils Rsamtools]; };
exomeCopy = derive2 { name="exomeCopy"; version="1.28.0"; sha256="1y475ka8lkf3mh4xj0qvgk0nd0gf497dym9bvl5wpss1fqsks6im"; depends=[GenomeInfoDb GenomicRanges IRanges Rsamtools]; };
@ -1074,7 +1074,7 @@ in with self; {
fgsea = derive2 { name="fgsea"; version="1.8.0"; sha256="0cxxvlmg340l5l5fz4abbwppiri0ibg4navvq5k3wg511mz8ma2q"; depends=[BiocParallel data_table fastmatch ggplot2 gridExtra Matrix Rcpp]; };
flagme = derive2 { name="flagme"; version="1.38.1"; sha256="1llzkq5944kgh32xns67f8bcfvpgia809b1ly1nfhpa2mpfsvyr1"; depends=[CAMERA gcspikelite gplots MASS SparseM xcms]; };
flipflop = derive2 { name="flipflop"; version="1.20.0"; sha256="100ia0j4ir61ihriyz36jnxpa9s4ivs35fifs4yzfiysf7lma3al"; depends=[GenomicRanges IRanges Matrix]; };
flowAI = derive2 { name="flowAI"; version="1.12.3"; sha256="1n6l6q1vmnh9lbb00bafbi76pq1q5rfjpqlaws2si5ybsp4vwkqa"; depends=[changepoint flowCore ggplot2 knitr plyr RColorBrewer reshape2 rmarkdown scales]; };
flowAI = derive2 { name="flowAI"; version="1.12.7"; sha256="1s4mll9zdn84dlf08p91lacs70rijq2rv717f2rk6m71a48l6ac4"; depends=[changepoint flowCore ggplot2 knitr plyr RColorBrewer reshape2 rmarkdown scales]; };
flowBeads = derive2 { name="flowBeads"; version="1.20.1"; sha256="06w9lfsam3mv9gv6qigsjw9vl169kcyaa7vrh2ii138gry20b9qz"; depends=[Biobase flowCore knitr rrcov xtable]; };
flowBin = derive2 { name="flowBin"; version="1.18.1"; sha256="1fdj5ziyc10fp27jarx18z97vxnf7d5zy2nwbia6x441svrvc534"; depends=[BiocGenerics class flowCore flowFP limma snow]; };
flowCHIC = derive2 { name="flowCHIC"; version="1.16.1"; sha256="1472c1jdg9zk94pw84nbr8042rh7k7mrdbyjncqcigrx12dhgdh6"; depends=[EBImage flowCore ggplot2 hexbin vegan]; };
@ -1156,13 +1156,13 @@ in with self; {
goSTAG = derive2 { name="goSTAG"; version="1.6.1"; sha256="0ib9a1v9zblysmk7a6wrg6cj1q6is2s9mranb28nn2r067kfx77l"; depends=[AnnotationDbi biomaRt GO_db memoise]; };
goTools = derive2 { name="goTools"; version="1.56.0"; sha256="0w2mb8g5fnn7vm35cqw437f2sdiba4c72ay1n7frh0z1xc7hqc3r"; depends=[AnnotationDbi GO_db]; };
goseq = derive2 { name="goseq"; version="1.34.1"; sha256="1j87j98cajcjqabv6rb6zmcqxsqxxhbb3w60w1iink4rhsh8m3mn"; depends=[AnnotationDbi BiasedUrn BiocGenerics geneLenDataBase GO_db mgcv]; };
gpart = derive2 { name="gpart"; version="1.0.0"; sha256="0dgv8g5vxzab4ax1aqvs7bjrd52i299jvxrdfxrswxdrsl7jj0ad"; depends=[AnnotationDbi biomaRt data_table GenomicRanges Homo_sapiens igraph IRanges OrganismDbi Rcpp TxDb_Hsapiens_UCSC_hg38_knownGene]; };
gpart = derive2 { name="gpart"; version="1.0.1"; sha256="0p9cz9x1w9i3y4zjrznw67r2gdh1slm4j2m2wxzga3y9d8wi8s8m"; depends=[AnnotationDbi biomaRt data_table GenomicRanges Homo_sapiens igraph IRanges OrganismDbi Rcpp TxDb_Hsapiens_UCSC_hg38_knownGene]; };
gpls = derive2 { name="gpls"; version="1.54.0"; sha256="14sffq2h6hqlzaq1nzw34rkg7nnshfp6k5r3wyvavq6k25384jr0"; depends=[]; };
gprege = derive2 { name="gprege"; version="1.26.0"; sha256="0b2zrxggljfgr8w2ns7h80ymqrvfi8kaliy32k2najm089kpv8dy"; depends=[gptk]; };
graph = derive2 { name="graph"; version="1.60.0"; sha256="1kgnsm6f0vmb9qbkmmrnvxbwqc0gar17dq5gv1v10hrksw6mh64i"; depends=[BiocGenerics]; };
graphite = derive2 { name="graphite"; version="1.28.2"; sha256="0jdi5s7ffl7snwxrbk1nj8vb4db5wv328ipypyl8ddrzk6rljcy5"; depends=[AnnotationDbi checkmate graph httr rappdirs]; };
groHMM = derive2 { name="groHMM"; version="1.16.0"; sha256="1ph92fv44b90v7mk4b1mjvv0dlrhl8ba01klxbnd0vs4qn9zxplh"; depends=[GenomeInfoDb GenomicAlignments GenomicRanges IRanges MASS rtracklayer S4Vectors]; };
gsean = derive2 { name="gsean"; version="1.2.0"; sha256="01f3wlv2gr28hd9cmyaf7z7pd08hf7i3849blxmy04b9k9a35md3"; depends=[fgsea PPInfer]; };
gsean = derive2 { name="gsean"; version="1.2.1"; sha256="0amx19163pfff16hncphh4nccdp7br2f1v5ddzynzx8drslywz1p"; depends=[fgsea PPInfer]; };
gtrellis = derive2 { name="gtrellis"; version="1.14.0"; sha256="17c43vs6m6hj90x5is0pbcpcv59gg9z98c47hnvlypgcqch38h6v"; depends=[circlize GenomicRanges GetoptLong IRanges]; };
gwascat = derive2 { name="gwascat"; version="2.14.0"; sha256="1fnyjydhicq4ayrv0lqjv48h9bd72h40s6l82g1h2ng0icwz38g0"; depends=[AnnotationDbi AnnotationHub BiocGenerics Biostrings GenomeInfoDb GenomicFeatures GenomicRanges ggbio ggplot2 gQTLstats graph Gviz Homo_sapiens IRanges Rsamtools rtracklayer S4Vectors snpStats SummarizedExperiment VariantAnnotation]; };
gwasurvivr = derive2 { name="gwasurvivr"; version="1.0.0"; sha256="0f1p2l6ypbrnaqlmqsjz5rfa6afd4kqhkrniqi7hfwjza7myrcvp"; depends=[GWASTools matrixStats SNPRelate SummarizedExperiment survival VariantAnnotation]; };
@ -1192,7 +1192,7 @@ in with self; {
iClusterPlus = derive2 { name="iClusterPlus"; version="1.18.0"; sha256="08w6f1ad1mc05ws7jdq1j6sn3rflbdp1q5nii09a6qjx83micr4n"; depends=[]; };
iGC = derive2 { name="iGC"; version="1.12.0"; sha256="1m3mhxkvxsswmk6sqd78brx94pwyzc3z71kv2dzxj1409g6s1h25"; depends=[data_table plyr]; };
iPAC = derive2 { name="iPAC"; version="1.26.0"; sha256="01s5sgkid33jhzkjk7mdkdn48asp4ibj8b9r5cx5f3ngmkbfpdql"; depends=[Biostrings gdata multtest scatterplot3d]; };
iSEE = derive2 { name="iSEE"; version="1.2.1"; sha256="1vg6z0kjd45zj8zi392fzmrxwnylxy8ggp9d83qcanwzkdi743va"; depends=[AnnotationDbi BiocGenerics colourpicker cowplot dplyr DT ggplot2 igraph mgcv rentrez reshape2 rintrojs S4Vectors scales shiny shinyAce shinydashboard shinyjs SingleCellExperiment SummarizedExperiment vipor viridisLite]; };
iSEE = derive2 { name="iSEE"; version="1.2.3"; sha256="0z8shqcca3mgs3p2mnmrmd3v4q2gabdsm5a7x4s3n30vl8pfck88"; depends=[AnnotationDbi BiocGenerics colourpicker cowplot dplyr DT ggplot2 igraph mgcv rentrez reshape2 rintrojs S4Vectors scales shiny shinyAce shinydashboard shinyjs SingleCellExperiment SummarizedExperiment vipor viridisLite]; };
iSeq = derive2 { name="iSeq"; version="1.34.0"; sha256="0hlslyypijb4w9m01xkn6r8svs0kkp4nbv4xdz844pvyyxcn4afc"; depends=[]; };
iasva = derive2 { name="iasva"; version="1.0.1"; sha256="1cmbsa75fhs5zxjlfijwknk5s5i6w9q7r7xn34m3hz0y9asg62fc"; depends=[BiocParallel cluster irlba SummarizedExperiment]; };
ibh = derive2 { name="ibh"; version="1.30.0"; sha256="0wghj4qbnfg7zy1pbz580x9m1wszlhiyc34s9sd4q5spviz8dxh5"; depends=[simpIntLists]; };
@ -1239,7 +1239,7 @@ in with self; {
lumi = derive2 { name="lumi"; version="2.34.0"; sha256="1fpmjpgcy5n0hx9whn9m3jhjmciqq0l59nvy5addbq0a4wnjhx8q"; depends=[affy annotate AnnotationDbi Biobase DBI GenomicFeatures GenomicRanges KernSmooth lattice MASS methylumi mgcv nleqslv preprocessCore RSQLite]; };
mAPKL = derive2 { name="mAPKL"; version="1.12.0"; sha256="1bp8xpcrz7d76lazp72p25rzp3gcmr2z4cyhcgbg678gpsp61lj9"; depends=[AnnotationDbi apcluster Biobase clusterSim e1071 igraph limma multtest parmigene reactome_db]; };
mBPCR = derive2 { name="mBPCR"; version="1.36.0"; sha256="0vsb87518x770li85jdkns1qsabmixsn8mvh96hamr0adcwvgzrz"; depends=[Biobase oligoClasses SNPchip]; };
mCSEA = derive2 { name="mCSEA"; version="1.2.1"; sha256="10qa9xvqnkgh8clddp3ifj31xgykilhnn4xqhfmnrk3k2l9dsgzj"; depends=[fgsea GenomicFeatures GenomicRanges ggplot2 Gviz Homo_sapiens IRanges limma mCSEAdata S4Vectors SummarizedExperiment]; };
mCSEA = derive2 { name="mCSEA"; version="1.2.2"; sha256="0lan3ycvlg2z21wih4dnmiiq2al0jspqbv974pfak57s8h6vznrj"; depends=[fgsea GenomicFeatures GenomicRanges ggplot2 Gviz Homo_sapiens IRanges limma mCSEAdata S4Vectors SummarizedExperiment]; };
maCorrPlot = derive2 { name="maCorrPlot"; version="1.52.0"; sha256="11gg32sj2iyd3l7hxlqlhgd8adcgsfdz7n5lypsz1d7d3y760f7y"; depends=[lattice]; };
maPredictDSC = derive2 { name="maPredictDSC"; version="1.20.0"; sha256="00m792cgx3v6gp81axpqf48bdxkl8l2gnl6fvsx3xbsk4akm33p2"; depends=[affy AnnotationDbi caret class e1071 gcrma hgu133plus2_db limma LungCancerACvsSCCGEO MASS ROC ROCR]; };
maSigPro = derive2 { name="maSigPro"; version="1.54.0"; sha256="15bndkrwafj1vg2ik0s5003dzs65ibyhgz79ya5gry0b5h365qri"; depends=[Biobase MASS mclust venn]; };
@ -1271,7 +1271,7 @@ in with self; {
metaSeq = derive2 { name="metaSeq"; version="1.22.1"; sha256="00jwcgcx250v9glqxc1d0cvydn2jqzxxq62jmwskv87av68ppqbs"; depends=[NOISeq Rcpp snow]; };
metabomxtr = derive2 { name="metabomxtr"; version="1.16.1"; sha256="1nz1higya3i7lbmqgxv5fa4nxwpm7b2fvsa69x52b36i0z70y7lc"; depends=[Biobase BiocParallel Formula ggplot2 multtest optimx plyr]; };
metagene = derive2 { name="metagene"; version="2.14.0"; sha256="09krnp862jz8mgjyp6v5ynvsrl4asfvzsvi21rj8af5b0ywkwvwg"; depends=[BiocParallel data_table DBChIP EnsDb_Hsapiens_v86 ensembldb GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 gplots IRanges magrittr matrixStats muStat purrr R6 Rsamtools rtracklayer stringr]; };
metagenomeFeatures = derive2 { name="metagenomeFeatures"; version="2.2.1"; sha256="0mja44akzn9xzvwdiia368cyxpdmc67zsqim0mjsml9ip8ar5im6"; depends=[ape Biobase Biostrings dbplyr DECIPHER dplyr lattice lazyeval magrittr purrr RSQLite S4Vectors stringr]; };
metagenomeFeatures = derive2 { name="metagenomeFeatures"; version="2.2.3"; sha256="0dirj9xsn13jz572j0z37997s3nhgb3l1gqm67giarbp1h0nw20l"; depends=[ape Biobase Biostrings dbplyr DECIPHER dplyr lattice lazyeval magrittr RSQLite S4Vectors stringr]; };
metagenomeSeq = derive2 { name="metagenomeSeq"; version="1.24.1"; sha256="0zsb9vilmkvmx7vhw4074qgkxi5xd0kihzx2q5bi7l2zjd152y78"; depends=[Biobase foreach glmnet gplots limma Matrix matrixStats RColorBrewer]; };
metahdep = derive2 { name="metahdep"; version="1.40.0"; sha256="02xw6pb6688hhgq3213s55sb73qmd6xjfaqk7bz4ci7m4ilf6c2k"; depends=[]; };
metaseqR = derive2 { name="metaseqR"; version="1.22.1"; sha256="0nrvm55jx25mwrdg9p52mlbvvcqcvkbg2z1i9g5fhb0c7llcrldx"; depends=[baySeq biomaRt brew corrplot DESeq EDASeq edgeR gplots limma log4r NBPSeq NOISeq qvalue rjson vsn]; };
@ -1280,7 +1280,7 @@ in with self; {
methVisual = derive2 { name="methVisual"; version="1.34.0"; sha256="09ss0s5z950m6v2y037v8qwsp238w73302ls1xh9ps8gkz05a800"; depends=[Biostrings ca gridBase gsubfn IRanges plotrix sqldf]; };
methimpute = derive2 { name="methimpute"; version="1.4.1"; sha256="1xcparys2ifv2y5rp8ih558l8apnw5b3mjnkkc29szf38mzk9a1r"; depends=[Biostrings data_table GenomeInfoDb GenomicRanges ggplot2 IRanges minpack_lm Rcpp reshape2]; };
methyAnalysis = derive2 { name="methyAnalysis"; version="1.24.0"; sha256="0afgaf3xl2dnpl86agbx44fiq4i5i96535p3hd9y845xdq5ymvnp"; depends=[annotate AnnotationDbi Biobase BiocGenerics biomaRt genefilter GenomeInfoDb GenomicFeatures GenomicRanges genoset Gviz IRanges lumi methylumi org_Hs_eg_db rtracklayer SummarizedExperiment VariantAnnotation]; };
methylGSA = derive2 { name="methylGSA"; version="1.0.2"; sha256="11wrks3fc9fyrchcc41203d6yfkd8cvigi5w4di2hxdzijg8qlm2"; depends=[AnnotationDbi clusterProfiler ggplot2 GO_db IlluminaHumanMethylation450kanno_ilmn12_hg19 IlluminaHumanMethylationEPICanno_ilm10b2_hg19 missMethyl org_Hs_eg_db reactome_db RobustRankAggreg stringr]; };
methylGSA = derive2 { name="methylGSA"; version="1.0.3"; sha256="112m7i1q0iwlcsi27vfcgvchrqvjlhqr613hmf7j03wwxwdjr1bd"; depends=[AnnotationDbi clusterProfiler ggplot2 GO_db IlluminaHumanMethylation450kanno_ilmn12_hg19 IlluminaHumanMethylationEPICanno_ilm10b2_hg19 missMethyl org_Hs_eg_db reactome_db RobustRankAggreg stringr]; };
methylInheritance = derive2 { name="methylInheritance"; version="1.6.1"; sha256="0n11jkka37aqmirn73hl8kabilb220i1pv10i62jzq623sqpdsz9"; depends=[BiocParallel GenomicRanges ggplot2 gridExtra IRanges methylKit rebus S4Vectors]; };
methylKit = derive2 { name="methylKit"; version="1.8.1"; sha256="1zcfwy7i10aqgnf7r0c41hakb5aai3s3n9y8pc6a98vimz51ly2z"; depends=[data_table emdbook fastseg GenomeInfoDb GenomicRanges gtools IRanges KernSmooth limma mclust qvalue R_utils Rcpp Rhtslib Rsamtools rtracklayer S4Vectors zlibbioc]; };
methylMnM = derive2 { name="methylMnM"; version="1.20.0"; sha256="0sd3vj58yfscngpcl9hys2nys3siq1h2ask5r8j6jx6yz3qs91xd"; depends=[edgeR statmod]; };
@ -1297,17 +1297,17 @@ in with self; {
miRSM = derive2 { name="miRSM"; version="1.0.0"; sha256="09z2ca1qpf2m3s5cc59y4xzcixlbl847c17lx1kmrakabqpsxy8i"; depends=[BiBitR BicARE biclust Biobase dynamicTreeCut fabia flashClust GFA GSEABase iBBiG igraph isa2 linkcomm MCL miRsponge NMF PMA Rcpp rqubic runibic s4vd SummarizedExperiment WGCNA]; };
miRcomp = derive2 { name="miRcomp"; version="1.12.0"; sha256="17b6bq70d6ly09vma5mdlk54620jdxw6k4bwdyxgghyk7kwmd753"; depends=[Biobase KernSmooth miRcompData]; };
miRmine = derive2 { name="miRmine"; version="1.4.0"; sha256="0zfdm5d6ifkq55v38xcjwzq19ifh6jgbg1pjp298mn15yjsjzfj1"; depends=[SummarizedExperiment]; };
miRsponge = derive2 { name="miRsponge"; version="1.8.0"; sha256="0j1ab8pw9sa8pm53b1z8kx5pj3jkiw6lncv8cj77g0zcwg3f7xpw"; depends=[clusterProfiler corpcor DOSE igraph linkcomm MCL Rcpp ReactomePA survival varhandle]; };
miRsponge = derive2 { name="miRsponge"; version="1.8.1"; sha256="1nxcdmsvbn0y0pgv74xl3lp6sgddax2mrh2hrqvz7q0hm1gljd26"; depends=[clusterProfiler corpcor DOSE igraph linkcomm MCL org_Hs_eg_db Rcpp ReactomePA survival varhandle]; };
microRNA = derive2 { name="microRNA"; version="1.40.0"; sha256="1asrjljh4bxgzvbgnp72sqyqv13kvzbfdn3jy01v3l98dppjnwsf"; depends=[Biostrings]; };
microbiome = derive2 { name="microbiome"; version="1.4.2"; sha256="0amla1m69axhlslbg1pbvl61qyxb6qjpdfd5g2j8b116h8xrmyab"; depends=[dplyr ggplot2 phyloseq reshape2 tidyr vegan]; };
mimager = derive2 { name="mimager"; version="1.6.0"; sha256="097fv7wfj0wj0chijcl5v52lf35pc48va1ddsq6qii5xzi626cpd"; depends=[affy affyPLM Biobase BiocGenerics DBI gtable oligo oligoClasses preprocessCore S4Vectors scales]; };
minet = derive2 { name="minet"; version="3.40.0"; sha256="0hb1k3p750qykmqjz59yjak5h8vmnln8zcp2dffjnqvwgn78i23w"; depends=[infotheo]; };
minfi = derive2 { name="minfi"; version="1.28.3"; sha256="0la40n72i7r6mip8lsnnnv84l1pp07p7bhmhlqnm5zirin03lxh6"; depends=[beanplot Biobase BiocGenerics BiocParallel Biostrings bumphunter data_table DelayedArray DelayedMatrixStats genefilter GenomeInfoDb GenomicRanges GEOquery HDF5Array illuminaio IRanges lattice limma MASS mclust nlme nor1mix preprocessCore quadprog RColorBrewer reshape S4Vectors siggenes SummarizedExperiment]; };
minfi = derive2 { name="minfi"; version="1.28.4"; sha256="1sjwwqb0syngvj75saaky9y06hbxsawhhcmfvavzkhicxipafv7r"; depends=[beanplot Biobase BiocGenerics BiocParallel Biostrings bumphunter data_table DelayedArray DelayedMatrixStats genefilter GenomeInfoDb GenomicRanges GEOquery HDF5Array illuminaio IRanges lattice limma MASS mclust nlme nor1mix preprocessCore quadprog RColorBrewer reshape S4Vectors siggenes SummarizedExperiment]; };
mirIntegrator = derive2 { name="mirIntegrator"; version="1.12.0"; sha256="1vgl2kz4jahrw885gib7yaxwliij1ric9mmsad8v4zravw7d9knj"; depends=[AnnotationDbi ggplot2 graph org_Hs_eg_db Rgraphviz ROntoTools]; };
missMethyl = derive2 { name="missMethyl"; version="1.16.0"; sha256="0axssdkyvdfpq7r47sckbbp7w8wa06j1ncskcn2w9f95nl1dbya5"; depends=[AnnotationDbi BiasedUrn GO_db IlluminaHumanMethylation450kanno_ilmn12_hg19 IlluminaHumanMethylation450kmanifest IlluminaHumanMethylationEPICanno_ilm10b4_hg19 IlluminaHumanMethylationEPICmanifest limma methylumi minfi org_Hs_eg_db ruv statmod stringr]; };
missRows = derive2 { name="missRows"; version="1.2.0"; sha256="0fgw36358z0lc0ppkpy49vw1p2k2w3ji01apff8gpkfb310zipwc"; depends=[ggplot2 gtools MultiAssayExperiment plyr S4Vectors]; };
mitoODE = derive2 { name="mitoODE"; version="1.20.1"; sha256="17cppvvvbpa4k62wrih3q61mrkc3145d5macq0sp6vh2vag61xdm"; depends=[KernSmooth MASS minpack_lm mitoODEdata]; };
mixOmics = derive2 { name="mixOmics"; version="6.6.1"; sha256="1i21dxg30jvn3p8mhswcq0y326hxapcvhrphh98wwpxmbmnk4bhd"; depends=[corpcor dplyr ellipse ggplot2 gridExtra igraph lattice MASS matrixStats rARPACK RColorBrewer reshape2 tidyr]; };
mixOmics = derive2 { name="mixOmics"; version="6.6.2"; sha256="00mq3ikxnx8msgvciqjzis5n83klbzkp5nlk47hl41zksxnyknwm"; depends=[corpcor dplyr ellipse ggplot2 gridExtra igraph lattice MASS matrixStats rARPACK RColorBrewer reshape2 tidyr]; };
mogsa = derive2 { name="mogsa"; version="1.16.0"; sha256="14rl7md4bdpb24cxj5pmr196dy0amih8l4611kgwbrvdm9k13d3s"; depends=[Biobase BiocGenerics cluster corpcor genefilter gplots graphite GSEABase svd]; };
monocle = derive2 { name="monocle"; version="2.10.1"; sha256="0shwkgqs93j2l5h36yyvb1lf724107cfjrmzp5fxfj1lqc0y61lf"; depends=[Biobase BiocGenerics biocViews cluster combinat DDRTree densityClust dplyr fastICA ggplot2 HSMMSingleCell igraph irlba limma MASS Matrix matrixStats pheatmap plyr proxy qlcMatrix RANN Rcpp reshape2 Rtsne slam stringr tibble VGAM viridis]; };
mosaics = derive2 { name="mosaics"; version="2.20.0"; sha256="1536y2fizmi7jafq7bhbv8bzpf5b97dfskpg9a7v4c9xv6isagnx"; depends=[GenomeInfoDb GenomicAlignments GenomicRanges IRanges lattice MASS Rcpp Rsamtools S4Vectors]; };
@ -1332,7 +1332,7 @@ in with self; {
mygene = derive2 { name="mygene"; version="1.18.0"; sha256="03knrfbqm9hr30l3s58jkqyl6sl83p1vf4zyahr1ld0qrw81pvx7"; depends=[GenomicFeatures Hmisc httr jsonlite plyr S4Vectors sqldf]; };
myvariant = derive2 { name="myvariant"; version="1.12.0"; sha256="1vsp8m6rwyk09i0rg5j8w29vgn5hzz7fh8gc2fbjbg3icls26gn8"; depends=[GenomeInfoDb Hmisc httr jsonlite magrittr plyr S4Vectors VariantAnnotation]; };
mzID = derive2 { name="mzID"; version="1.20.1"; sha256="15yd4bdxprw3kg7zj2k652y3yr3si781iw28jqvnkm0gsc23rd0c"; depends=[doParallel foreach iterators plyr ProtGenerics XML]; };
mzR = derive2 { name="mzR"; version="2.16.1"; sha256="0mlwg646k49klxrznckzfv54a9mz6irj42fqpaaa0xjm6cw2lwaa"; depends=[Biobase BiocGenerics ncdf4 ProtGenerics Rcpp Rhdf5lib zlibbioc]; };
mzR = derive2 { name="mzR"; version="2.16.2"; sha256="19fn58zl59kd0hsjjc6y975y9187nfls0028a4k3v0s9wfg5b3vn"; depends=[Biobase BiocGenerics ncdf4 ProtGenerics Rcpp Rhdf5lib zlibbioc]; };
ncdfFlow = derive2 { name="ncdfFlow"; version="2.28.1"; sha256="1nabfa8nz6plw8w2xfla0xffqmxyk699dbv9615cazhf6vl6289f"; depends=[BH Biobase BiocGenerics flowCore flowViz Rcpp RcppArmadillo Rhdf5lib zlibbioc]; };
ndexr = derive2 { name="ndexr"; version="1.4.1"; sha256="067x2sj3pnq3hrxjpw4y4qp9gimgymxik9zdqjkirix77h817682"; depends=[httr igraph jsonlite plyr tidyr]; };
nem = derive2 { name="nem"; version="2.56.0"; sha256="02j5rm0h9bjghgba244k0acshbnhrr38ghvx6cmf8za8fw19k3v2"; depends=[boot e1071 graph limma plotrix RBGL RColorBrewer Rgraphviz statmod]; };
@ -1381,7 +1381,7 @@ in with self; {
pathVar = derive2 { name="pathVar"; version="1.12.0"; sha256="09ncdyamlhs24yyg7fnb77vchqxpxh6asmj32pxhpvkkkgq106p4"; depends=[data_table EMT ggplot2 gridExtra Matching mclust]; };
pathifier = derive2 { name="pathifier"; version="1.20.0"; sha256="064q5nbxgyz4hx6h4f92w7vyd77pndmxadwa8cw9y5qzh9g29a5m"; depends=[princurve R_oo]; };
pathprint = derive2 { name="pathprint"; version="1.12.0"; sha256="06lv35nx0d098idjnlcr5bziilwnpapbbcsdfrwglcibgqis9hzh"; depends=[]; };
pathview = derive2 { name="pathview"; version="1.22.1"; sha256="19xvlk4sm0jf2xdl1cm2v8i1acxp8xk2yzpjgwv8r6x5h13zqpf0"; depends=[AnnotationDbi graph KEGGgraph KEGGREST org_Hs_eg_db png Rgraphviz XML]; };
pathview = derive2 { name="pathview"; version="1.22.3"; sha256="1dw87ldd3awc8br61012iaifznby5qq3i8v333blqspfb4mnmjyy"; depends=[AnnotationDbi graph KEGGgraph KEGGREST org_Hs_eg_db png Rgraphviz XML]; };
paxtoolsr = derive2 { name="paxtoolsr"; version="1.16.0"; sha256="0sa680x51kcsbmlrb54z8m1qn1pjyzx7k26pni17mfdzaw1q9jki"; depends=[httr igraph jsonlite plyr R_utils readr rJava rjson XML]; };
pcaExplorer = derive2 { name="pcaExplorer"; version="2.8.1"; sha256="1af9yf4nnsn3wb93zb0agn2vr04ianhm85326fl6qm51pmjljswh"; depends=[AnnotationDbi biomaRt d3heatmap DESeq2 DT genefilter GenomicRanges ggplot2 ggrepel GO_db GOstats IRanges knitr limma NMF pheatmap plyr rmarkdown S4Vectors scales shiny shinyAce shinyBS shinydashboard SummarizedExperiment threejs tidyr topGO]; };
pcaGoPromoter = derive2 { name="pcaGoPromoter"; version="1.26.0"; sha256="0rdj9043zdvfh2gwas13i6787kw01m1cr998prgf12n9l107v68s"; depends=[AnnotationDbi Biostrings ellipse]; };
@ -1460,7 +1460,7 @@ in with self; {
rTANDEM = derive2 { name="rTANDEM"; version="1.22.1"; sha256="1nfh0423jfzf44acqn3jlnl3561lkxwjxv6i7y3h5j4zi3309q2z"; depends=[data_table Rcpp XML]; };
rTRM = derive2 { name="rTRM"; version="1.20.0"; sha256="1alz54x6vxsm7mhsasn1cviad0gbg3vlrzm3m5mf9rj61nlz6zgd"; depends=[AnnotationDbi DBI igraph RSQLite]; };
rTRMui = derive2 { name="rTRMui"; version="1.20.0"; sha256="09rc2kvcpi7c0b0dmq07byrd5208szwm4nvisdr8xhnhcsxq8f51"; depends=[MotifDb org_Hs_eg_db org_Mm_eg_db rTRM shiny]; };
rWikiPathways = derive2 { name="rWikiPathways"; version="1.2.0"; sha256="19sndn705580cg6idwnw9rbr92cgl83lv0zbvdaxnrvly22i9242"; depends=[caTools httr RJSONIO]; };
rWikiPathways = derive2 { name="rWikiPathways"; version="1.2.1"; sha256="090mf50r9r1xwvirxwr1p9cv410q8h5pawv9v5kbnmwqi2b6qvzd"; depends=[caTools httr RJSONIO XML]; };
rain = derive2 { name="rain"; version="1.16.0"; sha256="02grbm9c8q34np24218myzv0zgkq4p37mynpkm6c6xncywijgcsi"; depends=[gmp multtest]; };
rama = derive2 { name="rama"; version="1.56.0"; sha256="0ns6dczyj8zglrfni1i0sfiqhpcii5h6hdv8yjg0hkm29g2qjzd0"; depends=[]; };
ramwas = derive2 { name="ramwas"; version="1.6.0"; sha256="19iqh994x28mninyfay6rkjib947w9wjhsz1ac528w9paqjyk0ha"; depends=[BiocGenerics biomaRt Biostrings digest filematrix GenomicAlignments glmnet KernSmooth Rsamtools]; };
@ -1469,7 +1469,7 @@ in with self; {
rcellminer = derive2 { name="rcellminer"; version="2.4.0"; sha256="1r627fhzzjvjzdj8y0cxr65csj023c1jwl04jnj2i3g2g4pzcicl"; depends=[Biobase fingerprint ggplot2 gplots rcdk rcellminerData shiny stringr]; };
readat = derive2 { name="readat"; version="1.8.0"; sha256="0sg4dccxkyl7arlfhd0qmq1kx5f1sykvi822ssh0brp8yjj1hx53"; depends=[assertive_base assertive_files assertive_numbers assertive_properties assertive_sets assertive_types Biobase data_table dplyr magrittr openxlsx pathological reshape2 stringi SummarizedExperiment testthat tidyr]; };
reb = derive2 { name="reb"; version="1.60.0"; sha256="1a62sfl0hw9nqw25b7hv76m9bn5l56d0sin1ii9s4qa2hj67nwxy"; depends=[Biobase idiogram]; };
recount = derive2 { name="recount"; version="1.8.1"; sha256="1aziihmg3jq3qrkvg39fmx4wawmpdgvcp8f4zxnl6fq1p2p2rfw3"; depends=[BiocParallel derfinder downloader GenomeInfoDb GenomicRanges GEOquery IRanges RCurl rentrez rtracklayer S4Vectors SummarizedExperiment]; };
recount = derive2 { name="recount"; version="1.8.2"; sha256="0cnvbbpgijx30p7ma2gi508nvi8w7cli29p9af6lvn3q395fs9ya"; depends=[BiocParallel derfinder downloader GenomeInfoDb GenomicRanges GEOquery IRanges RCurl rentrez rtracklayer S4Vectors SummarizedExperiment]; };
recoup = derive2 { name="recoup"; version="1.10.1"; sha256="0s4lhxffaai3l0rs4h62zcn0y5kxnmqxvcdnin726q3sc75b7h7l"; depends=[BiocGenerics biomaRt circlize ComplexHeatmap GenomicAlignments GenomicRanges ggplot2 plyr rtracklayer]; };
regionReport = derive2 { name="regionReport"; version="1.16.1"; sha256="1c4yf6nda4i9h4mapskfnxrrzgv5ic8bkbwyssd650vx840agj99"; depends=[BiocStyle DEFormats derfinder DESeq2 GenomeInfoDb GenomicRanges knitcitations knitr knitrBootstrap RefManageR rmarkdown S4Vectors SummarizedExperiment]; };
regioneR = derive2 { name="regioneR"; version="1.14.0"; sha256="19la74swgzxp90z2nr3pzsgkxd7wp70zl6i2ipv3plg841f6k5zd"; depends=[Biostrings BSgenome GenomeInfoDb GenomicRanges IRanges memoise rtracklayer S4Vectors]; };
@ -1490,7 +1490,7 @@ in with self; {
rqt = derive2 { name="rqt"; version="1.8.0"; sha256="08kics4hq4y23ydilafylm2rmbnh88hj02rrd5bbl5685as724vn"; depends=[car CompQuadForm glmnet Matrix metap pls ropls RUnit SummarizedExperiment]; };
rqubic = derive2 { name="rqubic"; version="1.28.0"; sha256="0va7263mxij13qyjmqrv9hxbgxig17hjw1617v0gzrcprs978735"; depends=[biclust Biobase BiocGenerics]; };
rsbml = derive2 { name="rsbml"; version="2.40.0"; sha256="04brk985cdf6psr8ixkqahg9nmb7lrv1jfy0j1c84l2znskya77f"; depends=[BiocGenerics graph]; };
rtracklayer = derive2 { name="rtracklayer"; version="1.42.1"; sha256="1ycmcxvgvszvjv75hlmg0i6pq8i7r8720vgmfayb905s9l6j82x6"; depends=[BiocGenerics Biostrings GenomeInfoDb GenomicAlignments GenomicRanges IRanges RCurl Rsamtools S4Vectors XML XVector zlibbioc]; };
rtracklayer = derive2 { name="rtracklayer"; version="1.42.2"; sha256="1c76g6h9lx2nm7dvb2zp9dmrpk3vanx3zaz6q9clggpj7yj5lmjd"; depends=[BiocGenerics Biostrings GenomeInfoDb GenomicAlignments GenomicRanges IRanges RCurl Rsamtools S4Vectors XML XVector zlibbioc]; };
runibic = derive2 { name="runibic"; version="1.4.0"; sha256="1s1zbcbfxbchrh8h9602n5gh8ji8zqll9kfd4wg3w3668ckv7vx3"; depends=[biclust Rcpp SummarizedExperiment testthat]; };
sRAP = derive2 { name="sRAP"; version="1.22.0"; sha256="0qgskdizjh8z15qx4lvrdy5rg7h20hdg454n2wqvpmrk6wvp0ylp"; depends=[gplots pls qvalue ROCR WriteXLS]; };
sSeq = derive2 { name="sSeq"; version="1.20.1"; sha256="08f59qg96qkndrlkdyk3i495i00gcx5kj1jcdy6zqkm9j7km88y2"; depends=[caTools RColorBrewer]; };
@ -1512,7 +1512,7 @@ in with self; {
scone = derive2 { name="scone"; version="1.6.1"; sha256="0l1x4cjnfjbpx6k55sjqx03555daa6v63rq0rg6b7jpz8xxzwa7p"; depends=[aroma_light BiocParallel boot class cluster compositions diptest edgeR fpc gplots hexbin limma matrixStats mixtools rARPACK RColorBrewer rhdf5 RUVSeq SummarizedExperiment]; };
scoreInvHap = derive2 { name="scoreInvHap"; version="1.4.0"; sha256="03d7pny3qkcs279869yry8rkw7js3xyrc8b7p4i7hlpzd44x25a3"; depends=[BiocParallel Biostrings GenomicRanges snpStats SummarizedExperiment VariantAnnotation]; };
scran = derive2 { name="scran"; version="1.10.2"; sha256="07mgilr3gq3lnrm1fjm9zhz4w7970bjhsykln1drqy9gkzj5sn7g"; depends=[beachmat BiocGenerics BiocNeighbors BiocParallel DelayedArray DelayedMatrixStats dynamicTreeCut edgeR igraph limma Matrix Rcpp Rhdf5lib S4Vectors scater SingleCellExperiment statmod SummarizedExperiment]; };
scruff = derive2 { name="scruff"; version="1.0.1"; sha256="0m7lab7ac1jvp4y092rsyrr4l40gdrqi92khhkq30261f2fm6cf6"; depends=[AnnotationDbi BiocGenerics BiocParallel Biostrings data_table GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggbio ggplot2 ggthemes plyr refGenome Rsamtools S4Vectors scales ShortRead SingleCellExperiment stringdist SummarizedExperiment]; };
scruff = derive2 { name="scruff"; version="1.0.1"; sha256="0m7lab7ac1jvp4y092rsyrr4l40gdrqi92khhkq30261f2fm6cf6"; depends=[AnnotationDbi BiocGenerics BiocParallel Biostrings data_table GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggbio ggplot2 ggthemes plyr Rsamtools S4Vectors scales ShortRead SingleCellExperiment stringdist SummarizedExperiment]; };
scsR = derive2 { name="scsR"; version="1.18.0"; sha256="11mf5kv8mk1nlfxd081a7dx1v60yf94cg46b5bjflidp3qhrsi9g"; depends=[BiocGenerics Biostrings ggplot2 hash IRanges plyr RColorBrewer sqldf STRINGdb]; };
segmentSeq = derive2 { name="segmentSeq"; version="2.16.0"; sha256="0pljd8hn2vxcsh22wmv53a7wkw3cdxpdv8q4ksfj5mvasa2mmkvi"; depends=[abind baySeq GenomeInfoDb GenomicRanges IRanges Rsamtools S4Vectors ShortRead]; };
semisup = derive2 { name="semisup"; version="1.6.0"; sha256="0lizf5x3abv4g8j4jxmsbbdiqj4f4gybc3jvw7zz12bd3fsj3c1i"; depends=[SummarizedExperiment VGAM]; };
@ -1525,10 +1525,10 @@ in with self; {
seqbias = derive2 { name="seqbias"; version="1.30.0"; sha256="0jwlwqa1z2scnaqkrz5hmmakrjaajf4dwd875s7pswvacygiy859"; depends=[Biostrings GenomicRanges Rsamtools zlibbioc]; };
seqcombo = derive2 { name="seqcombo"; version="1.4.1"; sha256="0046www9rl5lswcjn6friijd5plj0p7bfg0y0qzqsz7gqpm3nj58"; depends=[Biostrings cowplot dplyr ggplot2 igraph magrittr rvcheck]; };
seqplots = derive2 { name="seqplots"; version="1.20.1"; sha256="0hp3x8gdw65wc73hc1rcxbaqypq2zd50axsvcviqfgdv2dcb2ph7"; depends=[BiocManager Biostrings BSgenome class DBI digest DT fields GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 gridExtra IRanges jsonlite kohonen plotrix RColorBrewer reshape2 Rsamtools RSQLite rtracklayer S4Vectors shiny]; };
seqsetvis = derive2 { name="seqsetvis"; version="1.2.0"; sha256="0wzgka604d6dgfqxmgqbc99441xnmywfcbnl22mx9r332y1wkasr"; depends=[data_table eulerr GenomicRanges ggplot2 IRanges limma png RColorBrewer Rsamtools rtracklayer S4Vectors]; };
seqsetvis = derive2 { name="seqsetvis"; version="1.2.1"; sha256="0x5410b3qwqn34lzs1x75ldlv6xmvdbjyxg8ja0gyg4hz5bc4vaj"; depends=[data_table eulerr GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 IRanges limma png RColorBrewer Rsamtools rtracklayer S4Vectors]; };
sesame = derive2 { name="sesame"; version="1.0.0"; sha256="01qxdnpkilxv18fpl3rizxri2l7crs62z8nd7ywhxfm6g4ch5l1z"; depends=[DNAcopy GenomicRanges ggplot2 illuminaio IRanges MASS preprocessCore R6 randomForest S4Vectors sesameData wheatmap]; };
sevenC = derive2 { name="sevenC"; version="1.2.0"; sha256="1p2xkv0n8hl9s4dlg54wgry73vnnlzylwximhan2ymnp3hgbg4j0"; depends=[BiocGenerics boot data_table GenomeInfoDb GenomicRanges InteractionSet IRanges purrr readr rtracklayer S4Vectors]; };
sevenbridges = derive2 { name="sevenbridges"; version="1.12.3"; sha256="1cwrqgixm6l83737fsdycqqyrap7xph8xp9m45hpcgh35z4d9r1y"; depends=[curl docopt dplyr httr jsonlite objectProperties S4Vectors stringr uuid yaml]; };
sevenbridges = derive2 { name="sevenbridges"; version="1.12.4"; sha256="14gwmfvbhyzywqmggc3s4g2f6vlxx28ndlibh3a4x7rrny04285i"; depends=[curl docopt dplyr httr jsonlite objectProperties S4Vectors stringr uuid yaml]; };
shinyMethyl = derive2 { name="shinyMethyl"; version="1.18.0"; sha256="0dzg1idkdy4x9h3z5yashrb03ad8ncjxz5j05jlaxx6k4aa7z8j8"; depends=[BiocGenerics IlluminaHumanMethylation450kmanifest matrixStats minfi RColorBrewer shiny]; };
shinyTANDEM = derive2 { name="shinyTANDEM"; version="1.20.1"; sha256="0lz4jr96g20fbrd34f9km6rj08yb2y09gp7zxnm0inlpdkvb4dby"; depends=[mixtools rTANDEM shiny xtable]; };
sigFeature = derive2 { name="sigFeature"; version="1.0.0"; sha256="0kjf4ss0baq4p7nn305szpvpdssagndxjmggdgfm6mfjsgfi5nj1"; depends=[BiocParallel biocViews e1071 Matrix nlme openxlsx pheatmap RColorBrewer SparseM SummarizedExperiment]; };
@ -1549,7 +1549,7 @@ in with self; {
skewr = derive2 { name="skewr"; version="1.14.0"; sha256="09132dwp8h3wdrf0agyc0vmby5z7c2hd3px4jrp9vgi2x1849mvn"; depends=[IlluminaHumanMethylation450kmanifest methylumi minfi mixsmsn RColorBrewer S4Vectors wateRmelon]; };
slalom = derive2 { name="slalom"; version="1.4.1"; sha256="0kb4y590cdph90k27av45jy889i3s1jarlhj57lyg8g14sr9sxq6"; depends=[BH ggplot2 GSEABase Rcpp RcppArmadillo rsvd SingleCellExperiment SummarizedExperiment]; };
slingshot = derive2 { name="slingshot"; version="1.0.0"; sha256="0nrqzsjwyk78cahw21x4i5lqac7h85k6nrq045nq4jmxyc977li3"; depends=[ape clusterExperiment igraph matrixStats princurve rgl SingleCellExperiment SummarizedExperiment]; };
slinky = derive2 { name="slinky"; version="1.0.0"; sha256="1b4pam8ajcc1zz1gxdz1gcjxrv75b60mwwhhvcfin3g9xfmgnkc3"; depends=[curl dplyr foreach httr jsonlite readr rhdf5 SummarizedExperiment tidyr]; };
slinky = derive2 { name="slinky"; version="1.0.2"; sha256="1bjs41p3a7ggk6brj2hih84p4qi8qd398xzrh1r8lrdwjy1cm6yl"; depends=[curl dplyr foreach httr jsonlite readr rhdf5 SummarizedExperiment tidyr]; };
snapCGH = derive2 { name="snapCGH"; version="1.52.0"; sha256="15fx1ryc6ab1aia768wpp8zhggfz2l9vildhkjh8chwaam1qd610"; depends=[aCGH cluster DNAcopy GLAD limma tilingArray]; };
snm = derive2 { name="snm"; version="1.30.0"; sha256="1qjd7g6c03rygp95cpry1m3yi83lyd57zp94whaymfriz39dx2i9"; depends=[corpcor lme4]; };
snpStats = derive2 { name="snpStats"; version="1.32.0"; sha256="1pplx4pf9bqi7v5v1l74yknc1s61carvbqkf327ky7vbvp0bck33"; depends=[BiocGenerics Matrix survival zlibbioc]; };
@ -1560,7 +1560,7 @@ in with self; {
spikeLI = derive2 { name="spikeLI"; version="2.42.0"; sha256="055zbrbh6wf3vvnc9p8px2ffz9wdhdg0h96260r7c72ax3v6wi5g"; depends=[]; };
spkTools = derive2 { name="spkTools"; version="1.38.0"; sha256="0rm2vlzid3wjm1g1kzmjklga1gcf852aznhxb1xr50v8drivkkz9"; depends=[Biobase gtools RColorBrewer]; };
splatter = derive2 { name="splatter"; version="1.6.1"; sha256="1kw9shzqwph44q2fksgp79mrjq23j3806clc4xydw3ys2w4kspj8"; depends=[akima BiocGenerics BiocParallel checkmate crayon edgeR fitdistrplus ggplot2 locfit matrixStats scales scater SingleCellExperiment SummarizedExperiment]; };
spliceSites = derive2 { name="spliceSites"; version="1.30.0"; sha256="1j40awy9irx53d1cdsx52pnxirjrrvgsj9zx5qhl2556ca65l26n"; depends=[Biobase BiocGenerics Biostrings doBy IRanges rbamtools refGenome seqLogo]; };
spliceSites = derive2 { name="spliceSites"; version="1.30.0"; sha256="1j40awy9irx53d1cdsx52pnxirjrrvgsj9zx5qhl2556ca65l26n"; depends=[Biobase BiocGenerics Biostrings doBy IRanges seqLogo]; };
splicegear = derive2 { name="splicegear"; version="1.54.0"; sha256="0phpkgjkc4c8lfr8xsciqyz7imsjpc3sxwsh95glxhrsm7i2mnip"; depends=[annotate Biobase XML]; };
splineTimeR = derive2 { name="splineTimeR"; version="1.10.0"; sha256="15dzhijkhpy7d8hwif59bic83fk6fnyjpp4qi7y7vwq139j6yaj2"; depends=[Biobase FIs GeneNet GSEABase gtools igraph limma longitudinal]; };
splots = derive2 { name="splots"; version="1.48.0"; sha256="0s10ha17p4yf6id0h0r0a2fk992jp4ah7v8ani689zy6pcc0w34d"; depends=[RColorBrewer]; };
@ -1604,7 +1604,7 @@ in with self; {
tracktables = derive2 { name="tracktables"; version="1.16.0"; sha256="160zh73yripvd150jfwm1xpk1amrg1qqjcyl8wwclpss0ks04ayb"; depends=[GenomicRanges IRanges RColorBrewer Rsamtools stringr tractor_base XML XVector]; };
transcriptR = derive2 { name="transcriptR"; version="1.10.1"; sha256="17m1i36jj7fdh4qqd29zia68q7yjhxgh47xndcbgbik78pfnnig7"; depends=[BiocGenerics caret chipseq e1071 GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 IRanges pROC reshape2 Rsamtools rtracklayer S4Vectors]; };
transcriptogramer = derive2 { name="transcriptogramer"; version="1.4.1"; sha256="1qd447glnwk3ysxnfjyn5i2smyq79mn6qgsa0klrgr3v1909ib57"; depends=[biomaRt data_table doSNOW foreach ggplot2 igraph limma progress RedeR snow tidyr topGO]; };
transite = derive2 { name="transite"; version="1.0.1"; sha256="09dwlgysgiyz8svfhfap17q3j7y8nh1bq5grq199dvrrs8ai8k80"; depends=[BiocGenerics Biostrings dplyr GenomicRanges ggplot2 ggseqlogo gridExtra Rcpp scales TFMPvalue]; };
transite = derive2 { name="transite"; version="1.0.2"; sha256="1xrkk7n6zgch24q1hx4fxj2z8ii5pfpakjmf5696v1w1d153415m"; depends=[BiocGenerics Biostrings dplyr GenomicRanges ggplot2 ggseqlogo gridExtra Rcpp scales TFMPvalue]; };
traseR = derive2 { name="traseR"; version="1.12.0"; sha256="1bf2cblagqkwsc66l9820kb7yh05bk62k0rplnqznnl36i5fw428"; depends=[BSgenome_Hsapiens_UCSC_hg19 GenomicRanges IRanges]; };
treeio = derive2 { name="treeio"; version="1.6.2"; sha256="0fvyj3m8yzq94cs2nhmmq6qvf7qqccxan2qkq764a9qlfrrpwa2c"; depends=[ape dplyr jsonlite magrittr rlang rvcheck tibble tidytree]; };
trena = derive2 { name="trena"; version="1.4.2"; sha256="1rrbkjizc4glp4ql30wn6ijmym4vxl3xda3ffy02maab1vg07mjp"; depends=[AnnotationDbi BiocParallel biomaRt Biostrings BSgenome BSgenome_Hsapiens_UCSC_hg19 BSgenome_Hsapiens_UCSC_hg38 BSgenome_Mmusculus_UCSC_mm10 DBI flare GenomicRanges glmnet lassopv MotifDb org_Hs_eg_db randomForest RMariaDB RPostgreSQL RSQLite SNPlocs_Hsapiens_dbSNP150_GRCh38 vbsr]; };
@ -1620,7 +1620,7 @@ in with self; {
tximport = derive2 { name="tximport"; version="1.10.1"; sha256="16wp09dm0cpb4mc00nmglfb8ica7qb4a55vm8ajgzyagbpfdd44l"; depends=[]; };
uSORT = derive2 { name="uSORT"; version="1.8.1"; sha256="1z6vlcgs83pc7388c6jwpm9dgv9rr95gsksqy5gaiyy0pa0bga8j"; depends=[Biobase BiocGenerics cluster fpc gplots igraph Matrix monocle plyr RANN RSpectra VGAM]; };
unifiedWMWqPCR = derive2 { name="unifiedWMWqPCR"; version="1.18.0"; sha256="110kb1g1kkfgk3nw099wyaww8l2jk3kk41bsz3gmbb2jni9v0ykx"; depends=[BiocGenerics HTqPCR]; };
universalmotif = derive2 { name="universalmotif"; version="1.0.13"; sha256="1k7xlp7mgkrsg0lxakhiwzq8jid2s01iaagav1yia9fninkgpp85"; depends=[ape BiocGenerics Biostrings ggplot2 ggseqlogo ggtree gtools processx Rcpp Rdpack]; };
universalmotif = derive2 { name="universalmotif"; version="1.0.22"; sha256="016r859xn2306zsckg0xpwv3ssngngw7drc27h7jhikmf5wkvbv1"; depends=[ape BiocGenerics Biostrings ggplot2 ggseqlogo ggtree gtools processx Rcpp Rdpack]; };
variancePartition = derive2 { name="variancePartition"; version="1.12.1"; sha256="18z6g633scn8p5s17nr02832i8kh7gvdx8pz1ggx4p5jpdh562v1"; depends=[Biobase colorRamps doParallel foreach ggplot2 gplots iterators limma lme4 lmerTest MASS pbkrtest reshape2 scales]; };
vbmp = derive2 { name="vbmp"; version="1.50.0"; sha256="08iyryhmahmm1p93c0kgvknf9gkd7i4l4jd3b9a234vwx5xy0zx2"; depends=[]; };
vidger = derive2 { name="vidger"; version="1.2.1"; sha256="1gz2v4zg6ry06msmxrr3f47i4gc2sfijrbkd0l5x7crp8a2mkcm3"; depends=[Biobase DESeq2 edgeR GGally ggplot2 ggrepel knitr RColorBrewer rmarkdown scales SummarizedExperiment tidyr]; };
@ -1635,7 +1635,7 @@ in with self; {
webbioc = derive2 { name="webbioc"; version="1.54.0"; sha256="16n6wc9q51wfpmh9y77p53sqdqdd8pn50c67vf6h4n7gv5wgnpwi"; depends=[affy annaffy Biobase BiocManager gcrma multtest qvalue vsn]; };
widgetTools = derive2 { name="widgetTools"; version="1.60.0"; sha256="0mz69pdr6q69avsvs6r5ncdkdmgwfislpil4v18dsflw4j454gwf"; depends=[]; };
wiggleplotr = derive2 { name="wiggleplotr"; version="1.6.1"; sha256="12fhbskkjwv4d9bdy3gab8n9pcf7qpwiwgx0248as445vfw8dil3"; depends=[assertthat cowplot dplyr GenomeInfoDb GenomicRanges ggplot2 IRanges purrr rtracklayer S4Vectors]; };
xcms = derive2 { name="xcms"; version="3.4.2"; sha256="1mqhv87y7316w9a9j50l82yr3cs3f71pj9a5kg90fzg5nc2d0i68"; depends=[Biobase BiocGenerics BiocParallel lattice MassSpecWavelet MSnbase multtest mzR plyr ProtGenerics RANN RColorBrewer robustbase S4Vectors]; };
xcms = derive2 { name="xcms"; version="3.4.4"; sha256="073f25m7y8z4560k93d99fv72pr7nrgrp054zssi7jhas4l3ddww"; depends=[Biobase BiocGenerics BiocParallel lattice MassSpecWavelet MSnbase multtest mzR plyr ProtGenerics RANN RColorBrewer robustbase S4Vectors]; };
xmapbridge = derive2 { name="xmapbridge"; version="1.40.0"; sha256="1a93vxrv9brfwv64wpiriwak1chlz6rg25dhcb9hyk2b8j8ky3ag"; depends=[]; };
xps = derive2 { name="xps"; version="1.42.0"; sha256="0x391j5rlihp64k5wslghlrw6vi4xwwjphskvl1k3iffda5yqknb"; depends=[]; };
yamss = derive2 { name="yamss"; version="1.8.1"; sha256="13pln09j08fjsr7bj17apy4j0sr79n7jzshi8jbnz57jil7k6ia9"; depends=[BiocGenerics data_table EBImage IRanges limma Matrix mzR S4Vectors SummarizedExperiment]; };

1921
pkgs/development/r-modules/cran-packages.nix generated
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1
pkgs/development/r-modules/default.nix
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@ -303,7 +303,6 @@ let
rapportools = [ pkgs.which ];
rapport = [ pkgs.which ];
readxl = [ pkgs.libiconv ];
rbamtools = [ pkgs.zlib.dev ];
rcdd = [ pkgs.gmp.dev ];
RcppCNPy = [ pkgs.zlib.dev ];
RcppGSL = [ pkgs.gsl_1 ];

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