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Merge pull request #224905 from NixOS/r-updates

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rPackages: CRAN repository changes and treewide update
This commit is contained in:
Justin Bedő 2023-04-08 06:45:19 +10:00 committed by GitHub
commit 86dc68fab4
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6 changed files with 3752 additions and 3614 deletions
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5
pkgs/build-support/fetchurl/mirrors.nix
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@ -43,6 +43,11 @@
"http://bioconductor.jp/packages/"
];
# CRAN mirrors
cran = [
"https://cran.r-project.org/src/contrib/"
];
# BitlBee mirrors, see https://www.bitlbee.org/main.php/mirrors.html
bitlbee = [
"https://get.bitlbee.org/"

96
pkgs/development/r-modules/bioc-packages.nix generated
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@ -17,7 +17,7 @@ in with self; {
AGDEX = derive2 { name="AGDEX"; version="1.46.0"; sha256="0yvdx32yr4mv7dl5ycpbxhrkm6csrr7k3398ggjavdcfhz54dgr8"; depends=[Biobase GSEABase]; };
AIMS = derive2 { name="AIMS"; version="1.30.0"; sha256="1civ4a14ynccv6xs27fm95fw6254l1z0q37546ivyv2mhbz0d2i1"; depends=[Biobase e1071]; };
ALDEx2 = derive2 { name="ALDEx2"; version="1.30.0"; sha256="0585s5pb8zr9il1vhxw9vjzzajmdcjmf9zz3zlc5vpczd3fnzfkf"; depends=[BiocParallel GenomicRanges IRanges multtest Rfast S4Vectors SummarizedExperiment zCompositions]; };
AMARETTO = derive2 { name="AMARETTO"; version="1.13.0"; sha256="18w65sf3h4yzw9v5xgkalxnkmgzgsx100v7qc7z4ifx10lgpji5n"; depends=[BiocFileCache callr circlize ComplexHeatmap curatedTCGAData doParallel dplyr DT foreach ggplot2 glmnet gridExtra httr impute knitr limma Matrix matrixStats MultiAssayExperiment Rcpp readr reshape2 rmarkdown tibble]; };
AMARETTO = derive2 { name="AMARETTO"; version="1.14.0"; sha256="06j75c4j71fkkw5s52nbzb3k084y2f4v4h3js9dgsxxrd6jkzfz9"; depends=[BiocFileCache callr circlize ComplexHeatmap curatedTCGAData doParallel dplyr DT foreach ggplot2 glmnet gridExtra httr impute knitr limma Matrix matrixStats MultiAssayExperiment Rcpp readr reshape2 rmarkdown tibble]; };
AMOUNTAIN = derive2 { name="AMOUNTAIN"; version="1.24.0"; sha256="0zzl5dv64yhdivsm2pgsfjikygib9pkfiv34h1lnmqrj6yivvvw8"; depends=[]; };
ANCOMBC = derive2 { name="ANCOMBC"; version="2.0.2"; sha256="0dlinv4vhxgni8ygzvfw8pbc6d1v9x5chhrpxblhs2c65bkgyxz5"; depends=[CVXR DescTools doParallel doRNG dplyr emmeans energy foreach Hmisc lme4 lmerTest magrittr MASS mia nloptr Rdpack rlang rngtools S4Vectors SingleCellExperiment SummarizedExperiment tibble tidyr TreeSummarizedExperiment]; };
ANF = derive2 { name="ANF"; version="1.20.0"; sha256="0yfwvgx7144r894fr13sx4gyyq6ljh7y734wx74sb7q80cl2gs1j"; depends=[Biobase igraph MASS RColorBrewer survival]; };
@ -45,14 +45,14 @@ in with self; {
AllelicImbalance = derive2 { name="AllelicImbalance"; version="1.36.0"; sha256="0zn8pp4pl5wr957mf6agjpn61f9qpnjx0nbxb5wnbr40672x0263"; depends=[AnnotationDbi BiocGenerics Biostrings BSgenome GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges gridExtra Gviz IRanges lattice latticeExtra nlme Rsamtools S4Vectors seqinr SummarizedExperiment VariantAnnotation]; };
AlphaBeta = derive2 { name="AlphaBeta"; version="1.12.0"; sha256="000apg879li9wkbyrl8cm73z6h0xasqp41h9ir9hywy2v38rmc5b"; depends=[BiocParallel data_table dplyr expm ggplot2 gtools igraph optimx plotly stringr]; };
AlpsNMR = derive2 { name="AlpsNMR"; version="4.0.4"; sha256="19j97qsa1vnxw05dlllbwzdap0xgnmgxyqbi5dy8w2ppwdzxgsfv"; depends=[baseline BiocParallel cli dplyr fs future generics ggplot2 glue htmltools magrittr matrixStats mixOmics pcaPP purrr readxl reshape2 rlang rmarkdown scales signal speaq stringr tibble tidyr tidyselect vctrs]; };
AnVIL = derive2 { name="AnVIL"; version="1.10.1"; sha256="0iqsffkrxv28g9cddx2w05f2dbscwxhh6bpizwa8xaxhvn5bcpsv"; depends=[BiocManager dplyr DT futile_logger htmltools httr jsonlite miniUI rapiclient rlang shiny tibble tidyr tidyselect]; };
AnVIL = derive2 { name="AnVIL"; version="1.10.2"; sha256="1j7n8c47j3njd5rnlrj8bkn4q5z7jpm0c9rdq1mlwd2i1yy9fz9b"; depends=[BiocManager dplyr DT futile_logger htmltools httr jsonlite miniUI rapiclient rlang shiny tibble tidyr tidyselect]; };
AnVILBilling = derive2 { name="AnVILBilling"; version="1.8.0"; sha256="13qcp2s012ai44dkddk71ga44y87jnl0vljyd93lj1dlh8nw7c00"; depends=[bigrquery DBI dplyr DT ggplot2 lubridate magrittr plotly shiny shinytoastr]; };
AnVILPublish = derive2 { name="AnVILPublish"; version="1.8.0"; sha256="1i5zf7pyrzi6v13gpscmdb5qdb5gknicc8fk9s9nmsl1wpj6wlsw"; depends=[AnVIL httr jsonlite readr rmarkdown whisker yaml]; };
Anaquin = derive2 { name="Anaquin"; version="2.22.0"; sha256="08y2syaacy15rxcf3x2r3906kfm58fkx7ainaqvy5inlc9f670j5"; depends=[DESeq2 ggplot2 knitr locfit plyr qvalue ROCR]; };
AneuFinder = derive2 { name="AneuFinder"; version="1.26.0"; sha256="154cg63n7h9h5jkj00aqf0hzbmmjg16bzvvk50fyixwq0a4q1j00"; depends=[AneuFinderData bamsignals BiocGenerics Biostrings cowplot DNAcopy doParallel ecp foreach GenomeInfoDb GenomicAlignments GenomicRanges ggdendro ggplot2 ggrepel IRanges mclust reshape2 Rsamtools S4Vectors]; };
AnnotationDbi = derive2 { name="AnnotationDbi"; version="1.60.2"; sha256="1c7f2vgdnh99zp83pvmghb7l0rihdijlhdj6ff992h7wrrha8lhg"; depends=[Biobase BiocGenerics DBI IRanges KEGGREST RSQLite S4Vectors]; };
AnnotationFilter = derive2 { name="AnnotationFilter"; version="1.22.0"; sha256="0m16kfssxbblf03ykawkmqa038cl90prhb23k6y88g2hwm00wynk"; depends=[GenomicRanges lazyeval]; };
AnnotationForge = derive2 { name="AnnotationForge"; version="1.40.1"; sha256="16wdcl56d5i8wrmin610kzs9ldy7h9w5fbnysjb1crkcgbikq1yy"; depends=[AnnotationDbi Biobase BiocGenerics DBI RCurl RSQLite S4Vectors XML]; };
AnnotationForge = derive2 { name="AnnotationForge"; version="1.40.2"; sha256="1ab7nl9zrlhlkwjrjr69zqq5hy9a8rp457hcr075n8qm5r5lf6wd"; depends=[AnnotationDbi Biobase BiocGenerics DBI RCurl RSQLite S4Vectors XML]; };
AnnotationHub = derive2 { name="AnnotationHub"; version="3.6.0"; sha256="1hk02q6mwx49khbhydndfa1qry8ylhmwz2dff8845a510hm0di7n"; depends=[AnnotationDbi BiocFileCache BiocGenerics BiocManager BiocVersion curl dplyr httr interactiveDisplayBase rappdirs RSQLite S4Vectors yaml]; };
AnnotationHubData = derive2 { name="AnnotationHubData"; version="1.28.0"; sha256="0mcx09kcxccw2gkf4c3w7sxgb7v3gwbvahvx9wgq8f93q85yzg95"; depends=[AnnotationDbi AnnotationForge AnnotationHub Biobase BiocCheck BiocGenerics BiocManager biocViews Biostrings DBI futile_logger GenomeInfoDb GenomicFeatures GenomicRanges graph IRanges jsonlite OrganismDbi RCurl Rsamtools RSQLite rtracklayer S4Vectors XML]; };
ArrayExpress = derive2 { name="ArrayExpress"; version="1.57.0"; sha256="1fzi951mjc4kbkkvlfvwlfrpfnjckkmw4xz4m5dapy1z2jkgp8w6"; depends=[Biobase limma oligo XML]; };
@ -104,7 +104,7 @@ in with self; {
BioMM = derive2 { name="BioMM"; version="1.14.0"; sha256="06c36lpbmcz0s8v6dsjbmlmisab3h02jx67ycwlnymfwzw1hq1cb"; depends=[BiocParallel CMplot e1071 ggplot2 glmnet imager lattice nsprcomp precrec ranger rms topGO vioplot xlsx]; };
BioMVCClass = derive2 { name="BioMVCClass"; version="1.66.0"; sha256="1xclmwxps7yvqnaw8kn6z4mlpx6v8xfzyly4cadsjaj2qm535xxk"; depends=[Biobase graph MVCClass Rgraphviz]; };
BioNAR = derive2 { name="BioNAR"; version="1.0.0"; sha256="1z0ln7j4ack0pv8bzxjfrq6ncsnd0jif5s42njm94c7j408fj9kz"; depends=[AnnotationDbi clusterCons dplyr fgsea ggplot2 ggrepel GO_db igraph latex2exp org_Hs_eg_db poweRlaw Rdpack RSpectra rSpectral scales stringr synaptome_db WGCNA]; };
BioNERO = derive2 { name="BioNERO"; version="1.6.0"; sha256="10nwgp8a9chn33p5k7cdp920rraiw187xfrylyd9bq010c7vp7xh"; depends=[BiocParallel ComplexHeatmap dynamicTreeCut GENIE3 ggnetwork ggnewscale ggplot2 ggrepel igraph intergraph matrixStats minet NetRep networkD3 patchwork RColorBrewer reshape2 SummarizedExperiment sva WGCNA]; };
BioNERO = derive2 { name="BioNERO"; version="1.6.1"; sha256="0ijdnl43cgzywgsz80jd6q0irixh6367qm1ll5ww1rcr4xas2nsl"; depends=[BiocParallel ComplexHeatmap dynamicTreeCut GENIE3 ggnetwork ggnewscale ggplot2 ggrepel igraph intergraph matrixStats minet NetRep networkD3 patchwork RColorBrewer reshape2 SummarizedExperiment sva WGCNA]; };
BioNet = derive2 { name="BioNet"; version="1.58.0"; sha256="12c6m7dzwkdh4bk1c5xmzm5ajrsba7v62mag1f3rrpmrapdh6s0j"; depends=[AnnotationDbi Biobase graph igraph RBGL]; };
BioNetStat = derive2 { name="BioNetStat"; version="1.18.0"; sha256="1h99d6gnqw5v9ha2169zfhw9cvxhyjgkf4zm8qj1i03h2cywapgv"; depends=[BiocParallel DT ggplot2 Hmisc igraph knitr markdown pathview pheatmap plyr psych RColorBrewer RJSONIO rmarkdown shiny shinyBS whisker yaml]; };
BioQC = derive2 { name="BioQC"; version="1.26.0"; sha256="1ssxsxdm8vmlrmvvdz5p98apd3xsal1h3ss8556g83kgw830zsxf"; depends=[Biobase edgeR Rcpp]; };
@ -119,7 +119,7 @@ in with self; {
BiocIO = derive2 { name="BiocIO"; version="1.8.0"; sha256="15d4xsn3k32q7lzcyxvs70f0jbh9fgwl3vi7xd6sqpggar12hh9f"; depends=[BiocGenerics S4Vectors]; };
BiocNeighbors = derive2 { name="BiocNeighbors"; version="1.16.0"; sha256="09f00rf5gwwlxxaycsciq4l53gjg5kjayx8xzhns2yf1fv297j9p"; depends=[BiocParallel Matrix Rcpp RcppHNSW S4Vectors]; };
BiocOncoTK = derive2 { name="BiocOncoTK"; version="1.18.0"; sha256="1x4mzzjvjgcxg5xyxjib8r2n55hpf2vzcci0xkb7d8frakfncn9s"; depends=[bigrquery car ComplexHeatmap curatedTCGAData DBI dplyr DT GenomicFeatures GenomicRanges ggplot2 ggpubr graph httr IRanges magrittr plyr Rgraphviz rjson S4Vectors scales shiny SummarizedExperiment]; };
BiocParallel = derive2 { name="BiocParallel"; version="1.32.5"; sha256="1yd6ln9cl3dcvfziar52fkvqi2lzm31l7j21r1rwl1mpkz0xapir"; depends=[BH codetools cpp11 futile_logger snow]; };
BiocParallel = derive2 { name="BiocParallel"; version="1.32.6"; sha256="1aq3b5fjs8j0d6nf3992a6gnzvmmaxbbkrj1im0k6ppsqac6dlj0"; depends=[BH codetools cpp11 futile_logger snow]; };
BiocPkgTools = derive2 { name="BiocPkgTools"; version="1.16.1"; sha256="0cl88adkbxv7sz07b8h5qpwwkwg85jx6xjinkd0yjac4xm7s4lyf"; depends=[BiocFileCache BiocManager biocViews dplyr DT gh graph htmltools htmlwidgets httr igraph jsonlite magrittr RBGL readr rlang rorcid rvest stringr tibble xml2]; };
BiocSet = derive2 { name="BiocSet"; version="1.12.1"; sha256="1cqp5m6yic5vsp8k05r50sx2cmi9cwzxfmlswcjw28nascq3gpv0"; depends=[AnnotationDbi BiocIO dplyr KEGGREST ontologyIndex plyr rlang S4Vectors tibble tidyr]; };
BiocSingular = derive2 { name="BiocSingular"; version="1.14.0"; sha256="041izymcifvi0pa97fh5000bwlyl0mdk9003i5bbvlld6mbbv2kk"; depends=[beachmat BiocGenerics BiocParallel DelayedArray irlba Matrix Rcpp rsvd S4Vectors ScaledMatrix]; };
@ -168,7 +168,7 @@ in with self; {
CNVMetrics = derive2 { name="CNVMetrics"; version="1.2.0"; sha256="11i47ml2y5s8adh3qysasjl8b3w4xhg5h7v9rcdmd1hysjl4d4hi"; depends=[BiocParallel GenomicRanges gridExtra IRanges magrittr pheatmap S4Vectors]; };
CNVPanelizer = derive2 { name="CNVPanelizer"; version="1.30.0"; sha256="02k6bbzaj7q87nsg9zqda8dz44q3wshsps5pzm2764gxcwn4sz0z"; depends=[BiocGenerics exomeCopy foreach GenomeInfoDb GenomicRanges ggplot2 gplots IRanges NOISeq openxlsx plyr reshape2 Rsamtools S4Vectors shiny shinyFiles shinyjs stringr testthat]; };
CNVRanger = derive2 { name="CNVRanger"; version="1.14.0"; sha256="1if6k9iakrvq0fw6j2xpd26l13ikkpni8px3w76c9z0wsvbjf0cc"; depends=[BiocGenerics BiocParallel data_table edgeR GDSArray gdsfmt GenomeInfoDb GenomicRanges IRanges lattice limma plyr qqman RaggedExperiment rappdirs reshape2 S4Vectors SNPRelate SummarizedExperiment]; };
CNVfilteR = derive2 { name="CNVfilteR"; version="1.12.1"; sha256="0jkd65ncsbgwrrg0xs8ycj2lm9ailrayqqd6a453sbhx74gjsnyy"; depends=[assertthat Biostrings CopyNumberPlots GenomeInfoDb GenomicRanges IRanges karyoploteR pracma regioneR Rsamtools SummarizedExperiment VariantAnnotation]; };
CNVfilteR = derive2 { name="CNVfilteR"; version="1.12.2"; sha256="07jjrzkf8bk20wb8wiw155bq0dhgnz24bhwzsdh2dakirmjhfpzb"; depends=[assertthat Biostrings CopyNumberPlots GenomeInfoDb GenomicRanges IRanges karyoploteR pracma regioneR Rsamtools SummarizedExperiment VariantAnnotation]; };
CNVgears = derive2 { name="CNVgears"; version="1.6.0"; sha256="0gqw8l7pswamjm4j1jr8ri1rpf31szlx9ba6b99j3iypisxq1r1r"; depends=[data_table ggplot2]; };
CNViz = derive2 { name="CNViz"; version="1.6.0"; sha256="1nm8k4ry8p6k8cb6bqi6dyffi48fyhv1gq1277cz1nys31y0pdnv"; depends=[CopyNumberPlots dplyr DT GenomicRanges karyoploteR magrittr plotly scales shiny]; };
CNVrd2 = derive2 { name="CNVrd2"; version="1.36.0"; sha256="0jr9m08ip17l9w9i62nqdv13p5f3s7n0zyj4y3vy671s6c1syfiv"; depends=[DNAcopy ggplot2 gridExtra IRanges rjags Rsamtools VariantAnnotation]; };
@ -245,7 +245,7 @@ in with self; {
CrispRVariants = derive2 { name="CrispRVariants"; version="1.26.0"; sha256="184bn5gyjj0s7wpnyrqxrsh47f7f9w020p5fbhbi48nnks38j7ca"; depends=[AnnotationDbi BiocParallel Biostrings GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 gridExtra IRanges reshape2 Rsamtools S4Vectors]; };
CyTOFpower = derive2 { name="CyTOFpower"; version="1.4.0"; sha256="0g3629xi5hvkds2ixibr9p2ipjyr341nksafh38ap2w870whc31j"; depends=[CytoGLMM diffcyt dplyr DT ggplot2 magrittr rlang shiny shinyFeedback shinyjs shinyMatrix SummarizedExperiment tibble tidyr]; };
CytoDx = derive2 { name="CytoDx"; version="1.18.0"; sha256="1w5xy40wpyw6fj42zj2zf79r0kkdhn6h7wxzilh1dhnqkd0k8ay1"; depends=[doParallel dplyr flowCore glmnet rpart rpart_plot]; };
CytoGLMM = derive2 { name="CytoGLMM"; version="1.6.0"; sha256="1vvzw440blicfmdidr1sh8wiyfwmgrhmvazikm4f7g8jcw0cn9dm"; depends=[BiocParallel caret cowplot doParallel dplyr factoextra flexmix ggplot2 ggrepel logging magrittr MASS Matrix mbest pheatmap RColorBrewer rlang speedglm stringr strucchange tibble tidyr]; };
CytoGLMM = derive2 { name="CytoGLMM"; version="1.6.0"; sha256="1vvzw440blicfmdidr1sh8wiyfwmgrhmvazikm4f7g8jcw0cn9dm"; depends=[BiocParallel caret cowplot doParallel dplyr factoextra flexmix ggplot2 ggrepel logging magrittr MASS Matrix mbest pheatmap RColorBrewer rlang stringr strucchange tibble tidyr]; };
CytoML = derive2 { name="CytoML"; version="2.10.0"; sha256="105vdmwwglknwk7x7cb6b2jf6bngbxsly0ymjf8175p2lfv98jsa"; depends=[BH Biobase cpp11 cytolib data_table dplyr flowCore flowWorkspace ggcyto graph jsonlite openCyto RBGL Rgraphviz Rhdf5lib RProtoBufLib tibble XML yaml]; };
DAMEfinder = derive2 { name="DAMEfinder"; version="1.10.1"; sha256="1cgykb70mxnhilwwp1jr4dr523zvjxpix173s4ldfh49064gzwc1"; depends=[BiocGenerics Biostrings bumphunter cowplot GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 IRanges limma plyr readr reshape2 Rsamtools S4Vectors stringr SummarizedExperiment VariantAnnotation]; };
DAPAR = derive2 { name="DAPAR"; version="1.30.6"; sha256="1z0p3aiypi5lpa4nam45klcf9dq8k18aig917w0v73ix3l88bmad"; depends=[Biobase DAPARdata foreach highcharter MSnbase]; };
@ -267,7 +267,7 @@ in with self; {
DExMA = derive2 { name="DExMA"; version="1.6.0"; sha256="04j5h3ijmhzkgs02r0vsq3p00i4ydcnnis4kn1a69bp3x1bnv0n9"; depends=[Biobase bnstruct DExMAdata GEOquery impute limma pheatmap plyr RColorBrewer scales snpStats sva swamp]; };
DFP = derive2 { name="DFP"; version="1.56.0"; sha256="1pkg4461ib1iplcrlwkwrqzdzqixj2rhwwfkhjw87z4rx04hz3gf"; depends=[Biobase]; };
DIAlignR = derive2 { name="DIAlignR"; version="2.6.0"; sha256="04kpdab8h0krxqzsxl3sb1gsxqwrrdpsn7irgdpns8qqjlzcbzv5"; depends=[ape bit64 data_table DBI dplyr ggplot2 magrittr mzR phangorn pracma Rcpp RcppEigen reticulate rlang RMSNumpress RSQLite signal tidyr zoo]; };
DMCFB = derive2 { name="DMCFB"; version="1.12.0"; sha256="00j362frx70vj326xjppkzfd36mvfq3ym58dnckz3c0jb2dxv3wr"; depends=[arm benchmarkme BiocParallel data_table fastDummies GenomicRanges IRanges MASS matrixStats rtracklayer S4Vectors speedglm SummarizedExperiment tibble]; };
DMCFB = derive2 { name="DMCFB"; version="1.12.0"; sha256="00j362frx70vj326xjppkzfd36mvfq3ym58dnckz3c0jb2dxv3wr"; depends=[arm benchmarkme BiocParallel data_table fastDummies GenomicRanges IRanges MASS matrixStats rtracklayer S4Vectors SummarizedExperiment tibble]; };
DMCHMM = derive2 { name="DMCHMM"; version="1.20.0"; sha256="1cf5i3ikn81qw0s3kbx2yl15fmgwal22yqpys8wya8pd2agbi4lj"; depends=[BiocParallel calibrate fdrtool GenomicRanges IRanges multcomp rtracklayer S4Vectors SummarizedExperiment]; };
DMRScan = derive2 { name="DMRScan"; version="1.20.0"; sha256="1mx0kk1rbn0mkk94mm1a7mk64ia315fvwwb34adyslmyq5gq93i5"; depends=[GenomeInfoDb GenomicRanges IRanges MASS Matrix mvtnorm RcppRoll]; };
DMRcaller = derive2 { name="DMRcaller"; version="1.30.0"; sha256="03d7rl5z1pxdwxya53mkf8a8n9jzp8rb8awhfhfd22dgdf2l327h"; depends=[betareg GenomicRanges IRanges Rcpp RcppRoll S4Vectors]; };
@ -327,13 +327,13 @@ in with self; {
EasyCellType = derive2 { name="EasyCellType"; version="1.0.0"; sha256="1xry2kgb7ha2hg82jap88px9xxcq609il85xi0k0gilla1swvjc1"; depends=[AnnotationDbi clusterProfiler dplyr forcats ggplot2 magrittr org_Hs_eg_db org_Mm_eg_db rlang]; };
EmpiricalBrownsMethod = derive2 { name="EmpiricalBrownsMethod"; version="1.26.0"; sha256="1vws49a204xkwixdvp5l62in7vxbpf4qsfcnm34zkc4kx5hval9j"; depends=[]; };
EnhancedVolcano = derive2 { name="EnhancedVolcano"; version="1.16.0"; sha256="1nbg2r097rz24ybzh9ww6myd6kc2rz02vbg6g0rb3dlng0002xsm"; depends=[ggplot2 ggrepel]; };
EnrichedHeatmap = derive2 { name="EnrichedHeatmap"; version="1.27.2"; sha256="1il5cj5zmjwp3drw9psj1nsp94yxd421kd7jqrv34p4r1v0zw5z5"; depends=[circlize ComplexHeatmap GenomicRanges GetoptLong IRanges locfit matrixStats Rcpp]; };
EnrichmentBrowser = derive2 { name="EnrichmentBrowser"; version="2.28.1"; sha256="1phcd2j19a7n2crqdigkh4bf8xn10drvsm1y6ny6hrk7scrnxz4j"; depends=[AnnotationDbi BiocFileCache BiocManager edgeR GO_db graph graphite GSEABase hwriter KEGGgraph KEGGREST limma pathview Rgraphviz S4Vectors safe SPIA SummarizedExperiment]; };
EnrichedHeatmap = derive2 { name="EnrichedHeatmap"; version="1.28.1"; sha256="0ikvs91qfswnyc2p6pn5b0n7rz0szx65pv0ywgzr94arm85gwirc"; depends=[circlize ComplexHeatmap GenomicRanges GetoptLong IRanges locfit matrixStats Rcpp]; };
EnrichmentBrowser = derive2 { name="EnrichmentBrowser"; version="2.28.2"; sha256="03z0ya3qsg4drsjiqb5akbjivbsmqjv8r52y8nhrc5kqa04zffxk"; depends=[AnnotationDbi BiocFileCache BiocManager edgeR GO_db graph graphite GSEABase hwriter KEGGgraph KEGGREST limma pathview Rgraphviz S4Vectors safe SPIA SummarizedExperiment]; };
EpiCompare = derive2 { name="EpiCompare"; version="1.2.0"; sha256="0h0ap1xa0g57zh4djr263d97firklsvb6nwq0dk1h39j8wyp5j54"; depends=[AnnotationHub BiocGenerics BRGenomics ChIPseeker data_table genomation GenomeInfoDb GenomicRanges ggplot2 htmltools IRanges plotly reshape2 rmarkdown rtracklayer stringr]; };
EpiDISH = derive2 { name="EpiDISH"; version="2.14.1"; sha256="02pf0y8sj1j48qfmfjckr4vx9rz3aypb6iydlpfvhcm829jr51cl"; depends=[e1071 locfdr MASS Matrix matrixStats quadprog stringr]; };
EpiMix = derive2 { name="EpiMix"; version="1.0.1"; sha256="1rn6hpxxiw8n7im2dnb2x19ahvahljxac6853qkwxb7a8gwvwlad"; depends=[AnnotationDbi AnnotationHub Biobase biomaRt data_table doParallel doSNOW downloader dplyr ELMER_data EpiMix_data ExperimentHub foreach GenomeInfoDb GenomicFeatures GenomicRanges GEOquery ggplot2 impute IRanges limma plyr progress R_matlab RColorBrewer RCurl rlang RPMM S4Vectors SummarizedExperiment tibble tidyr]; };
EpiTxDb = derive2 { name="EpiTxDb"; version="1.10.0"; sha256="152snn75nixdas9n3g80f32hmdrqdyv71cl8fkax5jl4mqrp6px5"; depends=[AnnotationDbi BiocFileCache BiocGenerics Biostrings curl DBI GenomeInfoDb GenomicFeatures GenomicRanges httr IRanges Modstrings RSQLite S4Vectors tRNAdbImport xml2]; };
EventPointer = derive2 { name="EventPointer"; version="3.6.0"; sha256="0z9bcqfwi8mym1pwywmvdmiszw0whpz4svh7jgwjvza94z5w5ly5"; depends=[abind affxparser Biostrings BSgenome cobs doParallel fgsea foreach GenomeInfoDb GenomicFeatures GenomicRanges glmnet graph igraph IRanges iterators limma lpSolve MASS Matrix matrixStats nnls poibin prodlim qvalue RBGL rhdf5 S4Vectors SGSeq speedglm stringr SummarizedExperiment tximport]; };
EventPointer = derive2 { name="EventPointer"; version="3.6.0"; sha256="0z9bcqfwi8mym1pwywmvdmiszw0whpz4svh7jgwjvza94z5w5ly5"; depends=[abind affxparser Biostrings BSgenome cobs doParallel fgsea foreach GenomeInfoDb GenomicFeatures GenomicRanges glmnet graph igraph IRanges iterators limma lpSolve MASS Matrix matrixStats nnls poibin prodlim qvalue RBGL rhdf5 S4Vectors SGSeq stringr SummarizedExperiment tximport]; };
ExCluster = derive2 { name="ExCluster"; version="1.16.0"; sha256="0m635as5xigkjqlmwh32afbbxffjf6ahrr83gr8z886z365h4m81"; depends=[GenomicRanges IRanges matrixStats Rsubread rtracklayer]; };
ExiMiR = derive2 { name="ExiMiR"; version="2.40.0"; sha256="02aw2kjpg2xfmx0xjphsalw81gixwd2yrw73rcbcxyz7fpq98c5h"; depends=[affy affyio Biobase limma preprocessCore]; };
ExperimentHub = derive2 { name="ExperimentHub"; version="2.6.0"; sha256="1j71zmxwiz82gg6kii2bmynzwll1r6fmsq972kmvxvm6crpvi15s"; depends=[AnnotationHub BiocFileCache BiocGenerics BiocManager curl rappdirs S4Vectors]; };
@ -592,8 +592,8 @@ in with self; {
MSPrep = derive2 { name="MSPrep"; version="1.8.0"; sha256="05bq27v2iwmrf92y6fyzczvnrwmpqy5b7faa3z4si68fhpa81p2s"; depends=[crmn dplyr magrittr missForest pcaMethods preprocessCore rlang S4Vectors stringr SummarizedExperiment sva tibble tidyr VIM]; };
MSnID = derive2 { name="MSnID"; version="1.32.0"; sha256="1ljhxbyq5pa32sh44f06cwcdq79xh5nm51bpx1i8xig3bvwyg7p9"; depends=[AnnotationDbi AnnotationHub Biobase BiocGenerics BiocStyle Biostrings data_table doParallel dplyr foreach ggplot2 iterators msmsTests MSnbase mzID mzR ProtGenerics purrr R_cache Rcpp reshape2 rlang RUnit stringr tibble xtable]; };
MSnbase = derive2 { name="MSnbase"; version="2.24.2"; sha256="0jdq41rhn9qyhxfihvrgim76fzdrycc02wjsjdrff42gmray49w7"; depends=[affy Biobase BiocGenerics BiocParallel digest ggplot2 impute IRanges lattice MALDIquant MASS MsCoreUtils mzID mzR pcaMethods plyr ProtGenerics Rcpp S4Vectors scales vsn XML]; };
MSstats = derive2 { name="MSstats"; version="4.6.3"; sha256="0zivmbkf5k21r0wg2p2gzhhb53qynf5yr2p4rd0dscb60ngsv0y3"; depends=[checkmate data_table ggplot2 ggrepel gplots limma lme4 marray MASS MSstatsConvert preprocessCore Rcpp RcppArmadillo survival]; };
MSstatsConvert = derive2 { name="MSstatsConvert"; version="1.8.2"; sha256="0nvmpjp4bf8gbx3701phfwlc8jjdnxdh9hi6vzsmn8sf0k43l6dk"; depends=[checkmate data_table log4r stringi]; };
MSstats = derive2 { name="MSstats"; version="4.6.5"; sha256="12gxr7615fp4yks0mqs6ikzhalihf0bq7kkc7sflpjqgzdv3jmws"; depends=[checkmate data_table ggplot2 ggrepel gplots limma lme4 marray MASS MSstatsConvert preprocessCore Rcpp RcppArmadillo statmod survival]; };
MSstatsConvert = derive2 { name="MSstatsConvert"; version="1.8.3"; sha256="1488vl6ijnb415510pa381206xjwzn64bjvvz4vm0s80h6bzpsix"; depends=[checkmate data_table log4r stringi]; };
MSstatsLOBD = derive2 { name="MSstatsLOBD"; version="1.6.0"; sha256="1hg9bjx9rwsdpj65mzd931lbyj4gb26x32mly4n1gkk1rf6iplry"; depends=[ggplot2 minpack_lm Rcpp]; };
MSstatsLiP = derive2 { name="MSstatsLiP"; version="1.4.1"; sha256="0hj10r3x1pql0497x3clk9wlv8xvbcvbv35q45x1ki8hfc5b3ifc"; depends=[Biostrings checkmate data_table dplyr factoextra ggplot2 ggpubr gridExtra MSstats MSstatsConvert MSstatsPTM purrr Rcpp scales stringr tibble tidyr tidyverse]; };
MSstatsPTM = derive2 { name="MSstatsPTM"; version="2.0.3"; sha256="1n0hf9xxqpq5yp23hdlv0ki919m69adr6a0m7577zx0icg30c0gy"; depends=[Biostrings checkmate data_table dplyr ggplot2 ggrepel gridExtra MSstats MSstatsConvert MSstatsTMT Rcpp stringr]; };
@ -670,7 +670,7 @@ in with self; {
NBSplice = derive2 { name="NBSplice"; version="1.15.0"; sha256="0yn7s7igshall34cflmdwvmknv8h1zdi6vg8svvcyn9fvzlgjdm8"; depends=[BiocParallel car edgeR ggplot2 MASS reshape2]; };
NCIgraph = derive2 { name="NCIgraph"; version="1.46.0"; sha256="06y04lbp1wn1w9xy3lsqcdsycp4cdlrcyhga5kn1a4skb48bc6rc"; depends=[graph KEGGgraph R_methodsS3 RBGL RCy3]; };
NOISeq = derive2 { name="NOISeq"; version="2.42.0"; sha256="1j0yafl5r1vsn99zkhvaz2mrwv37l4p8ldgiq09d9hxpjq9ls7i2"; depends=[Biobase Matrix]; };
NPARC = derive2 { name="NPARC"; version="1.10.0"; sha256="0zph5lxw7ysra897jkbrmxjvb4zd5q2knl07xw8q5dyphjw8bbr3"; depends=[BiocParallel broom dplyr magrittr MASS rlang tidyr]; };
NPARC = derive2 { name="NPARC"; version="1.10.1"; sha256="09xh883v929zabr6g1prr80885b4q0mhlvlw9mlycprrd8l2qch9"; depends=[BiocParallel broom dplyr magrittr MASS rlang tidyr]; };
NTW = derive2 { name="NTW"; version="1.48.0"; sha256="0vx5swxmw76vba5wwl1qjyyb2dm7vg9wa7jsky93knhdl0s2fli9"; depends=[mvtnorm]; };
NanoMethViz = derive2 { name="NanoMethViz"; version="2.4.2"; sha256="0qfw2smqqv6pj0a34plbxgdk49zh6nbf2r077hldbmp23ml6l6qj"; depends=[AnnotationDbi assertthat BiocSingular bsseq cpp11 data_table dplyr e1071 forcats fs GenomicRanges ggplot2 ggrastr glue limma patchwork purrr R_utils Rcpp readr rlang Rsamtools RSQLite S4Vectors scales scico stringr SummarizedExperiment tibble tidyr withr zlibbioc]; };
NanoStringDiff = derive2 { name="NanoStringDiff"; version="1.28.0"; sha256="1fjmp78q3hsnslarb7w39r3kcvf8m9jrzcw4na6k55dqp5917lys"; depends=[Biobase matrixStats Rcpp]; };
@ -757,7 +757,7 @@ in with self; {
PloGO2 = derive2 { name="PloGO2"; version="1.10.0"; sha256="0sq2x68bcslzldrh367hh9r1vrnk56mkc6iqiq3zy7rzgxhjigpl"; depends=[GO_db GOstats httr lattice openxlsx xtable]; };
PoDCall = derive2 { name="PoDCall"; version="1.6.0"; sha256="1x368wc96nn4k17kbbwavriqfp6qywxivdas6sp069c053xkjxrq"; depends=[diptest DT ggplot2 gridExtra LaplacesDemon mclust purrr readr rlist shiny shinyjs]; };
PoTRA = derive2 { name="PoTRA"; version="1.13.0"; sha256="1a32d1wndb24pxza3h53yddj9z2clff5srny2k00pbbfq1h99mjf"; depends=[BiocGenerics graph graphite igraph org_Hs_eg_db]; };
PrInCE = derive2 { name="PrInCE"; version="1.14.0"; sha256="07q3x6rx3raz187akwfdd01x57hxbf6njbrydnl9r6a8q0b0gb0b"; depends=[Biobase dplyr forecast Hmisc LiblineaR magrittr MSnbase naivebayes progress purrr ranger Rdpack robustbase speedglm tester tidyr]; };
PrInCE = derive2 { name="PrInCE"; version="1.14.0"; sha256="07q3x6rx3raz187akwfdd01x57hxbf6njbrydnl9r6a8q0b0gb0b"; depends=[Biobase dplyr forecast Hmisc LiblineaR magrittr MSnbase naivebayes progress purrr ranger Rdpack robustbase tester tidyr]; };
Prostar = derive2 { name="Prostar"; version="1.30.7"; sha256="10lzh7gib43f8l2a9p2bnvyf23llzm1931kpna1vpf6p1hswsxzv"; depends=[DAPAR DAPARdata data_table future ggplot2 gplots highcharter htmlwidgets later promises rhandsontable shiny shinyAce shinyBS shinycssloaders shinyjqui shinyjs shinythemes tibble vioplot webshot]; };
ProtGenerics = derive2 { name="ProtGenerics"; version="1.30.0"; sha256="1k5pg0zbhz9mjsl5i3j33p7qv2adax2lf7yqv6qz229fxxaxs5li"; depends=[]; };
ProteoDisco = derive2 { name="ProteoDisco"; version="1.4.0"; sha256="0df39hwg5kmc900b57dxw76mz11a7h4nb9kq1z1wl6ampx27w0ks"; depends=[BiocGenerics BiocParallel Biostrings checkmate cleaver dplyr GenomeInfoDb GenomicFeatures GenomicRanges IRanges ParallelLogger plyr rlang S4Vectors tibble tidyr VariantAnnotation XVector]; };
@ -805,7 +805,7 @@ in with self; {
RMassBank = derive2 { name="RMassBank"; version="3.8.0"; sha256="1zlv2vyarj0przwdn39iybk9fkghqbiic5y24i603jzajv9hqxz0"; depends=[assertthat Biobase ChemmineOB ChemmineR data_table digest enviPat httr logger MSnbase mzR R_utils rcdk Rcpp RCurl readJDX rjson S4Vectors webchem XML yaml]; };
RNAAgeCalc = derive2 { name="RNAAgeCalc"; version="1.10.0"; sha256="0zj6ham16bjycdh1qids0pfq6xdbp8y1hdjm966ba6cwl9xxwl5d"; depends=[AnnotationDbi ggplot2 impute org_Hs_eg_db recount SummarizedExperiment]; };
RNASeqPower = derive2 { name="RNASeqPower"; version="1.38.0"; sha256="1f8jiljxacqjj0vf2v01fclhl3i0w7xddxcs6ajxzlmmpqs19b8a"; depends=[]; };
RNASeqR = derive2 { name="RNASeqR"; version="1.15.1"; sha256="0rkn98mp6d9lzm82r37mixfq7vka71c9nwkzkixajpsba2915sh6"; depends=[ballgown Biostrings clusterProfiler corrplot DESeq2 DOSE edgeR factoextra FactoMineR ggplot2 gridExtra org_Hs_eg_db org_Sc_sgd_db pathview PerformanceAnalytics pheatmap rafalib reshape2 reticulate Rsamtools stringr systemPipeR systemPipeRdata]; };
RNASeqR = derive2 { name="RNASeqR"; version="1.16.0"; sha256="0m7d3mm644n81630v2m6vv7798x3rjshb9jcp63xq631j1wmk63i"; depends=[ballgown Biostrings clusterProfiler corrplot DESeq2 DOSE edgeR factoextra FactoMineR ggplot2 gridExtra org_Hs_eg_db org_Sc_sgd_db pathview PerformanceAnalytics pheatmap rafalib reshape2 reticulate Rsamtools stringr systemPipeR systemPipeRdata]; };
RNAdecay = derive2 { name="RNAdecay"; version="1.18.0"; sha256="1zf5gg25lyn4z8yq8mmysxzpm7jkpspawyv7siwzb0m80h59rpiy"; depends=[ggplot2 gplots nloptr scales TMB]; };
RNAinteract = derive2 { name="RNAinteract"; version="1.46.0"; sha256="18yhkkwq4gvwvph8pz53cl7id644vv1n2d3jngwrfk918jay5d0s"; depends=[abind Biobase cellHTS2 geneplotter gplots hwriter ICS ICSNP lattice latticeExtra limma locfit RColorBrewer splots]; };
RNAmodR = derive2 { name="RNAmodR"; version="1.12.0"; sha256="0xhz2fz0lw2yw14cw8fcnghk9y9q0v75b4bkf7bg5v0jrcgg6bc4"; depends=[BiocGenerics BiocParallel Biostrings BSgenome colorRamps GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 Gviz IRanges matrixStats Modstrings RColorBrewer reshape2 ROCR Rsamtools rtracklayer S4Vectors]; };
@ -825,7 +825,7 @@ in with self; {
RSeqAn = derive2 { name="RSeqAn"; version="1.18.0"; sha256="0fjcwm3fw13yv3vdawwdbmbqws3n47f5s10rcvllm3wrbb1zrwb6"; depends=[Rcpp]; };
RTCA = derive2 { name="RTCA"; version="1.50.0"; sha256="1jd5rknlbhdi650xg1isqxmgvi797c4jimn53x4nzaq88b8rabsc"; depends=[Biobase gtools RColorBrewer]; };
RTCGA = derive2 { name="RTCGA"; version="1.28.0"; sha256="1h7x1hb7lnjaq842k72l76j7l4d9130vfh8flvsjvzyc3l98cywq"; depends=[assertthat data_table dplyr ggplot2 ggthemes htmltools knitr purrr RCurl rmarkdown rvest scales stringi survival survminer viridis XML xml2]; };
RTCGAToolbox = derive2 { name="RTCGAToolbox"; version="2.28.0"; sha256="0w02191nj94wapywy43r33f04ck92mww49lg1gik38pbafaahv68"; depends=[BiocGenerics data_table DelayedArray GenomeInfoDb GenomicRanges httr limma RaggedExperiment RCircos RCurl RJSONIO rvest S4Vectors stringr SummarizedExperiment survival TCGAutils XML]; };
RTCGAToolbox = derive2 { name="RTCGAToolbox"; version="2.28.4"; sha256="14pw75cy4y5s6y2szdy8hwf8q1cysxiln6z45yn5lgdha96c6zdp"; depends=[BiocGenerics data_table DelayedArray GenomeInfoDb GenomicRanges httr limma RaggedExperiment RCircos RCurl RJSONIO rvest S4Vectors stringr SummarizedExperiment survival TCGAutils XML]; };
RTN = derive2 { name="RTN"; version="2.22.1"; sha256="0ga96f1qmbq5a8nxb94b60ml2fwynnz590xjbzcx1g5vhrblkj42"; depends=[car data_table igraph IRanges limma minet mixtools pheatmap pwr RedeR S4Vectors snow SummarizedExperiment viper]; };
RTNduals = derive2 { name="RTNduals"; version="1.22.0"; sha256="0m3h0rkix48pr4jywvm0h1pbqlv62gdzq3safwgqpgb7m0pg6d08"; depends=[RTN]; };
RTNsurvival = derive2 { name="RTNsurvival"; version="1.22.0"; sha256="00naywzamklldsvipyg3q2c16s84y8cw1bngdw2l1d8yra4qpq9r"; depends=[data_table dunn_test egg ggplot2 pheatmap RColorBrewer RTN RTNduals scales survival]; };
@ -886,7 +886,7 @@ in with self; {
Rtpca = derive2 { name="Rtpca"; version="1.8.0"; sha256="0n2k1pqba4fnf0mpkxywd93yzv9dk37c134pna3f25mgzgd84qj3"; depends=[Biobase dplyr fdrtool ggplot2 pROC tibble tidyr]; };
Rtreemix = derive2 { name="Rtreemix"; version="1.60.0"; sha256="0pkc4xsqqfdvszbb0xwx3hbxl1f7kcx3vm9bhjd7zkwls1jvv2n8"; depends=[Biobase graph Hmisc]; };
S4Vectors = derive2 { name="S4Vectors"; version="0.36.2"; sha256="131cg5fzrqgyp4kv260yn8hpr0zv5mxjhdnpl50ydgc2k0l43d38"; depends=[BiocGenerics]; };
SAIGEgds = derive2 { name="SAIGEgds"; version="1.12.4"; sha256="12cxrl47ka1h3b31f0i145shhxbiss976vzp78iw1ldh032sbdyh"; depends=[gdsfmt Rcpp RcppArmadillo RcppParallel SeqArray SPAtest]; };
SAIGEgds = derive2 { name="SAIGEgds"; version="1.12.5"; sha256="10cck00fc4wmj7iwzm0s5ddgm32rpw8f32fawqaigxxrb3r9yn20"; depends=[gdsfmt Rcpp RcppArmadillo RcppParallel SeqArray SPAtest]; };
SANTA = derive2 { name="SANTA"; version="2.34.0"; sha256="1i99s33id75srjr0x3yfz1gdyxw6766pr9w4afs8varfq8gxyc48"; depends=[igraph Matrix]; };
SBGNview = derive2 { name="SBGNview"; version="1.12.0"; sha256="0644hd9m4d1s9y000yh831pwyx7q1dzr69fjqf15bby78xkn70yn"; depends=[AnnotationDbi bookdown httr igraph KEGGREST knitr pathview Rdpack rmarkdown rsvg SBGNview_data SummarizedExperiment xml2]; };
SBMLR = derive2 { name="SBMLR"; version="1.94.0"; sha256="1x7p27abv9yc9mxbnprlwh5ph50jkycmlb90qib0mj361g4sr72d"; depends=[deSolve XML]; };
@ -896,7 +896,7 @@ in with self; {
SCATE = derive2 { name="SCATE"; version="1.8.0"; sha256="1zxliw0q979jps5lrmwks5m39qjd827jbvax1ndkd8p6lp1pcm2h"; depends=[GenomicAlignments GenomicRanges mclust preprocessCore Rtsne SCATEData splines2 xgboost]; };
SCArray = derive2 { name="SCArray"; version="1.6.0"; sha256="0crh2ddh87j5qbxnslr1f94nsf24rzqz61ng6v3g8zpsldkrw09b"; depends=[BiocGenerics DelayedArray DelayedMatrixStats gdsfmt IRanges S4Vectors SingleCellExperiment SummarizedExperiment]; };
SCBN = derive2 { name="SCBN"; version="1.16.0"; sha256="1lan5anf451dmb19sra79d4w2qi9kk7xw3zijswlbhfnd4fv9kgz"; depends=[]; };
SCFA = derive2 { name="SCFA"; version="1.8.0"; sha256="02g7hzgg68y8ckwhdwlp86574x0ffjp86nwg11whyira80v5y97y"; depends=[BiocParallel cluster coro glmnet igraph Matrix matrixStats psych RhpcBLASctl survival torch]; };
SCFA = derive2 { name="SCFA"; version="1.8.1"; sha256="1839mh15wxn07nh2zx7ahs2nimgxczpvn11dcr113zimxibm1r5z"; depends=[BiocParallel cluster coro glmnet igraph Matrix matrixStats psych RhpcBLASctl survival torch]; };
SCOPE = derive2 { name="SCOPE"; version="1.10.0"; sha256="1z9v27l8bs7gkbgp1kd1q9nyq77x46anc0x0c1as0m04qq7c5xbj"; depends=[BiocGenerics Biostrings BSgenome BSgenome_Hsapiens_UCSC_hg19 DescTools DNAcopy doParallel foreach GenomeInfoDb GenomicRanges gplots IRanges RColorBrewer Rsamtools S4Vectors]; };
SCnorm = derive2 { name="SCnorm"; version="1.20.0"; sha256="0zv4pf650crwliby34cjv7kxkrbqhc7xvz15n39hz5d0fk7ablgd"; depends=[BiocGenerics BiocParallel cluster data_table forcats ggplot2 moments quantreg S4Vectors SingleCellExperiment SummarizedExperiment]; };
SDAMS = derive2 { name="SDAMS"; version="1.18.0"; sha256="0i9i9w24qb66rbvkpjn2fin8x0mxd7g767i4ly0s75v9kbbp3ca6"; depends=[qvalue SummarizedExperiment trust]; };
@ -956,7 +956,7 @@ in with self; {
SimBindProfiles = derive2 { name="SimBindProfiles"; version="1.36.0"; sha256="12383rvcq7l2b3ik2gi741d33shrijj09gqpkbvbksj046j90swm"; depends=[Biobase limma mclust Ringo]; };
SimBu = derive2 { name="SimBu"; version="1.0.2"; sha256="0w8aksmcs16d6zmczarni8vrkw5b5kmv7n495w0qhmy6ync197bx"; depends=[basilisk BiocParallel data_table dplyr ggplot2 Matrix phyloseq proxyC RColorBrewer RCurl reticulate sparseMatrixStats SummarizedExperiment tidyr]; };
SimFFPE = derive2 { name="SimFFPE"; version="1.10.0"; sha256="1mlmlbnqqzxmjmir9lnqnqqb6hmj6wfxhy6wpmf6sv9y2vi2cvjz"; depends=[Biostrings doParallel dplyr foreach GenomicRanges IRanges Rsamtools truncnorm]; };
SingleCellExperiment = derive2 { name="SingleCellExperiment"; version="1.20.0"; sha256="1y9c9wf3009w4qh03zpsmc0ff0nkzal673a4nql5c11cn55sza2g"; depends=[BiocGenerics DelayedArray GenomicRanges S4Vectors SummarizedExperiment]; };
SingleCellExperiment = derive2 { name="SingleCellExperiment"; version="1.20.1"; sha256="1xwa6ncmqp21a4zx1dbs9p9b9rqbxhdgq2279mj4yl0gnpyqr9d7"; depends=[BiocGenerics DelayedArray GenomicRanges S4Vectors SummarizedExperiment]; };
SingleCellSignalR = derive2 { name="SingleCellSignalR"; version="1.10.0"; sha256="194gnss397wv3pxh1vf8gfikbz519l8hx3w4fm2hxvjs6q8k2234"; depends=[BiocManager circlize data_table edgeR foreach gplots igraph limma multtest pheatmap Rtsne scran SIMLR stringr]; };
SingleMoleculeFootprinting = derive2 { name="SingleMoleculeFootprinting"; version="1.6.0"; sha256="0dqyx3w8mxhf04xczzdv49lc2jkyamv1vlbdvfj0556y54z45cgg"; depends=[BiocGenerics Biostrings BSgenome data_table GenomeInfoDb GenomicRanges IRanges plyr QuasR RColorBrewer]; };
SingleR = derive2 { name="SingleR"; version="2.0.0"; sha256="05rw6l0d4n9m1dd7dp55zfripx036x1riwy83sx3aj5mw4r1awb6"; depends=[beachmat BiocNeighbors BiocParallel BiocSingular DelayedArray DelayedMatrixStats Matrix Rcpp S4Vectors SummarizedExperiment]; };
@ -969,10 +969,10 @@ in with self; {
SpatialExperiment = derive2 { name="SpatialExperiment"; version="1.8.1"; sha256="1kdsdk6n81n83bbbk4k8wqyj441d3xjbc4hqv1rpn8ny5mjcbpqg"; depends=[BiocFileCache BiocGenerics DropletUtils magick rjson S4Vectors SingleCellExperiment SummarizedExperiment]; };
SpatialFeatureExperiment = derive2 { name="SpatialFeatureExperiment"; version="1.0.3"; sha256="1616qpg31cnahj42s4gz435jj4j3d4rprr3bzxy58bdi7l2f8gv6"; depends=[BiocGenerics BiocParallel rjson S4Vectors sf SingleCellExperiment SpatialExperiment spdep SummarizedExperiment]; };
SpeCond = derive2 { name="SpeCond"; version="1.52.0"; sha256="09f5nz799ai7y4ig6y24xnldd37qvv7yd1k258z3s9ckc76cdgd4"; depends=[Biobase fields hwriter mclust RColorBrewer]; };
Spectra = derive2 { name="Spectra"; version="1.8.2"; sha256="0aj04f7lfs6fv34crxq49p98hvzvpggx3xlwic4s2227hswysfc0"; depends=[BiocGenerics BiocParallel fs IRanges MsCoreUtils ProtGenerics S4Vectors]; };
Spectra = derive2 { name="Spectra"; version="1.8.3"; sha256="1qib5rdyhgcs657hjnvp9zfhj05z3lpd3ngybqw3pikmc93ssf0h"; depends=[BiocGenerics BiocParallel fs IRanges MsCoreUtils ProtGenerics S4Vectors]; };
SpectralTAD = derive2 { name="SpectralTAD"; version="1.14.1"; sha256="1iml0by529cxhj6v82046l86affipar143ddk627b3p6a2sg35zr"; depends=[BiocParallel cluster dplyr GenomicRanges HiCcompare magrittr Matrix PRIMME]; };
SpidermiR = derive2 { name="SpidermiR"; version="1.28.0"; sha256="13dbz24g7l25d26piq00cpyll4cf8ss5l1kih7nvp8lrb540h6df"; depends=[AnnotationDbi gdata httr igraph miRNAtap miRNAtap_db org_Hs_eg_db]; };
SpliceWiz = derive2 { name="SpliceWiz"; version="1.0.2"; sha256="0d3d95pkk75pd076i275azhd1s0r8hrhki9xr9s4biihfa3f86ws"; depends=[AnnotationHub BiocFileCache BiocGenerics BiocParallel Biostrings BSgenome data_table DelayedArray DelayedMatrixStats DT fst genefilter GenomeInfoDb GenomicRanges ggplot2 HDF5Array heatmaply IRanges magrittr matrixStats NxtIRFdata ompBAM pheatmap plotly progress R_utils RColorBrewer Rcpp RcppProgress rhandsontable rhdf5 rtracklayer S4Vectors shiny shinydashboard shinyFiles shinyWidgets SummarizedExperiment XML zlibbioc]; };
SpliceWiz = derive2 { name="SpliceWiz"; version="1.0.4"; sha256="1lf9rcqplp6zzq11zvd1barcr0a99hfw0rgxlc93sg9gi8vm5xbn"; depends=[AnnotationHub BiocFileCache BiocGenerics BiocParallel Biostrings BSgenome data_table DelayedArray DelayedMatrixStats DT fst genefilter GenomeInfoDb GenomicRanges ggplot2 HDF5Array heatmaply IRanges magrittr matrixStats NxtIRFdata ompBAM pheatmap plotly progress R_utils RColorBrewer Rcpp RcppProgress rhandsontable rhdf5 rtracklayer S4Vectors shiny shinydashboard shinyFiles shinyWidgets SummarizedExperiment XML zlibbioc]; };
SplicingFactory = derive2 { name="SplicingFactory"; version="1.6.0"; sha256="1l92i96n7pgwrrl4ywwmbpl1al5x3lamn9wrplclkh0l8yx8c033"; depends=[SummarizedExperiment]; };
SplicingGraphs = derive2 { name="SplicingGraphs"; version="1.38.0"; sha256="0bqgn2lcmf6n188mj70cczwaps97dghmsililviq9sll91dj1gn8"; depends=[BiocGenerics BiocParallel GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges graph igraph IRanges Rgraphviz Rsamtools S4Vectors]; };
SpotClean = derive2 { name="SpotClean"; version="1.0.1"; sha256="1sxmj1zgx7xf3f29l9qws4sf9k6v1wwh94brawqd6qq1plv79g51"; depends=[dplyr ggplot2 Matrix RColorBrewer readbitmap rhdf5 rjson rlang S4Vectors Seurat SpatialExperiment SummarizedExperiment tibble viridis]; };
@ -1017,7 +1017,7 @@ in with self; {
TSCAN = derive2 { name="TSCAN"; version="1.36.0"; sha256="0aqn1rxzbil9m9mpcdfc0k75s5k6ljy0k4bjrn0zq3492zz4x1qi"; depends=[combinat DelayedArray fastICA ggplot2 gplots igraph Matrix mclust mgcv plyr S4Vectors shiny SingleCellExperiment SummarizedExperiment TrajectoryUtils]; };
TTMap = derive2 { name="TTMap"; version="1.20.0"; sha256="1vfj2zq4k4fzjnq48pckxkl3bwxwghhfwq8cz14hhwf10f735pq7"; depends=[Biobase colorRamps rgl SummarizedExperiment]; };
TVTB = derive2 { name="TVTB"; version="1.24.0"; sha256="16lhbbisgxmvp86qfkp0cdd8akjld0ryklw41hi3k4ndimzax6hf"; depends=[AnnotationFilter BiocGenerics BiocParallel Biostrings ensembldb ensemblVEP GenomeInfoDb GenomicRanges GGally ggplot2 Gviz IRanges limma reshape2 Rsamtools S4Vectors SummarizedExperiment VariantAnnotation]; };
TarSeqQC = derive2 { name="TarSeqQC"; version="1.27.0"; sha256="0iiv7c3jd1iw7i5nn65370zbvi11s9qn72zig9rw1gz8nvnmdgpq"; depends=[BiocGenerics BiocParallel Biostrings cowplot GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 Hmisc IRanges openxlsx plyr reshape2 Rsamtools S4Vectors]; };
TarSeqQC = derive2 { name="TarSeqQC"; version="1.28.0"; sha256="14ima8ymdb91lpkhdnsg6q7ajxs5p1xzzcsjfhixxkm341k45j35"; depends=[BiocGenerics BiocParallel Biostrings cowplot GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 Hmisc IRanges openxlsx plyr reshape2 Rsamtools S4Vectors]; };
TargetDecoy = derive2 { name="TargetDecoy"; version="1.4.0"; sha256="1xx9y5faf5ic14h7cnxpb83nr34mqzz0c846g1z28f3x9d0kg9kz"; depends=[ggplot2 ggpubr miniUI mzID mzR shiny]; };
TargetScore = derive2 { name="TargetScore"; version="1.36.0"; sha256="00z2zv5yhxriagvcz3bwkpr9ii0r9lw4vcf7kjp7x5pjzcc6q6wq"; depends=[Matrix pracma]; };
TargetSearch = derive2 { name="TargetSearch"; version="2.0.0"; sha256="1m5v2d67w0hi3x1b6nlsq97z197djnr23d6lj9krib1im70cclwy"; depends=[assertthat ncdf4]; };
@ -1090,7 +1090,7 @@ in with self; {
agilp = derive2 { name="agilp"; version="3.30.0"; sha256="15cw004g1vxfwvf939018vmlv9gym4r473jissamkygqdv78hcr0"; depends=[]; };
airpart = derive2 { name="airpart"; version="1.6.0"; sha256="07zxv0sjhlajaw4gxpjni14qyyqn70ar8ph5cpibzcky1lx6pmkl"; depends=[apeglm clue ComplexHeatmap dplyr dynamicTreeCut emdbook forestplot ggplot2 lpSolve matrixStats mclust pbapply plyr RColorBrewer rlang S4Vectors scater SingleCellExperiment smurf SummarizedExperiment]; };
alevinQC = derive2 { name="alevinQC"; version="1.14.0"; sha256="0rd64j4hkdk2d6mlld6qkv2m96lqc93807xjdf05xm8qkyx8g8y2"; depends=[cowplot dplyr DT GGally ggplot2 Rcpp rjson rlang rmarkdown shiny shinydashboard tximport]; };
alpine = derive2 { name="alpine"; version="1.24.0"; sha256="0rjnwljh4c2f7ml0m14pllns4pvyjwwf23qsn6zjygm5x04bapf0"; depends=[Biostrings GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges graph IRanges RBGL Rsamtools S4Vectors speedglm stringr SummarizedExperiment]; };
alpine = derive2 { name="alpine"; version="1.24.0"; sha256="0rjnwljh4c2f7ml0m14pllns4pvyjwwf23qsn6zjygm5x04bapf0"; depends=[Biostrings GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges graph IRanges RBGL Rsamtools S4Vectors stringr SummarizedExperiment]; };
altcdfenvs = derive2 { name="altcdfenvs"; version="2.60.0"; sha256="0fm4l93j6nm1w1w57zzryc1hkzapp8l16pkwjzdzllvwvsnsg8r0"; depends=[affy Biobase BiocGenerics Biostrings hypergraph makecdfenv S4Vectors]; };
amplican = derive2 { name="amplican"; version="1.20.0"; sha256="1c990i6gxbarcpbdpkz017x94spwzap95l95synlizbkyif4z8ij"; depends=[BiocGenerics BiocParallel Biostrings data_table dplyr GenomeInfoDb GenomicRanges ggplot2 ggthemes gridExtra gtable IRanges knitr Matrix matrixStats Rcpp rmarkdown S4Vectors ShortRead stringr waffle]; };
animalcules = derive2 { name="animalcules"; version="1.14.0"; sha256="1alpsamrglgvzhcibkaf7m3gyiv61wbj1gvsq4lw6vjka100j9qr"; depends=[ape assertthat biomformat caret covr DESeq2 dplyr DT forcats ggplot2 glmnet GUniFrac lattice limma magrittr Matrix MultiAssayExperiment plotly plotROC rentrez reshape2 S4Vectors scales shiny shinyjs SummarizedExperiment tibble tsne umap vegan XML]; };
@ -1155,7 +1155,7 @@ in with self; {
biodbNcbi = derive2 { name="biodbNcbi"; version="1.2.0"; sha256="0bjw5q9ls7p5pi13rzmax4iqfi5l7b0inga9b96bz18mcq071pqp"; depends=[biodb chk R6 XML]; };
biodbNci = derive2 { name="biodbNci"; version="1.2.0"; sha256="18kjpc71gis82hkg6h7jn0qqwc3m2dlc6ddmyr9cfmm1wvr3fdc6"; depends=[biodb chk R6 Rcpp testthat]; };
biodbUniprot = derive2 { name="biodbUniprot"; version="1.4.0"; sha256="1xg4f72maczqm2srscnzj3fhibnsya49d9a00d5r6qg1avc3g33v"; depends=[biodb R6]; };
biomaRt = derive2 { name="biomaRt"; version="2.54.0"; sha256="0c6agi652kbffqwd1r3c22ncisqaiy3gqbc9fz13767rr71im6lq"; depends=[AnnotationDbi BiocFileCache digest httr progress rappdirs stringr XML xml2]; };
biomaRt = derive2 { name="biomaRt"; version="2.54.1"; sha256="13nhp97cklaimc3cd931hz584nc58szk2gyxrkfhp7knfli6jbpi"; depends=[AnnotationDbi BiocFileCache digest httr progress rappdirs stringr XML xml2]; };
biomformat = derive2 { name="biomformat"; version="1.26.0"; sha256="0728fpj05bvna5lpm29pdbn4slfmq16nz35as086ddbl2hhc9ni1"; depends=[jsonlite Matrix plyr rhdf5]; };
biomvRCNS = derive2 { name="biomvRCNS"; version="1.38.0"; sha256="0n026b744ah5kcnipsyiqqs7vlz5n5im1kgv35i2pgxyzvf7a8sn"; depends=[GenomicRanges Gviz IRanges mvtnorm]; };
biosigner = derive2 { name="biosigner"; version="1.26.0"; sha256="11ncmxy4wqdg30w8a6dgcsywyzda49f9al435fz3pfj5rmlbbrlj"; depends=[Biobase e1071 MultiAssayExperiment MultiDataSet randomForest ropls SummarizedExperiment]; };
@ -1333,7 +1333,7 @@ in with self; {
dittoSeq = derive2 { name="dittoSeq"; version="1.10.0"; sha256="0sxpwg2cjw70pzdxbdw68nic521w65ryn83mj0pb2m1ncpimin4b"; depends=[colorspace cowplot ggplot2 ggrepel ggridges gridExtra pheatmap reshape2 S4Vectors SingleCellExperiment SummarizedExperiment]; };
divergence = derive2 { name="divergence"; version="1.14.0"; sha256="1khxmngdqsvn77hfiyz732q4z268qwk0r9ydmipz25lnddb25p7m"; depends=[SummarizedExperiment]; };
dks = derive2 { name="dks"; version="1.44.0"; sha256="1vg6xlw5ia6r1xycd5hrh6s2nxrkrgi34dsd1kfzhkf11d40ydfh"; depends=[cubature]; };
dmrseq = derive2 { name="dmrseq"; version="1.18.0"; sha256="1zx62lbj0am85p0c1vk06s7qf8294vk8yyh67nkiqc7xgqqwybyk"; depends=[AnnotationHub annotatr BiocParallel bsseq bumphunter DelayedMatrixStats GenomeInfoDb GenomicRanges ggplot2 IRanges locfit matrixStats nlme outliers RColorBrewer rtracklayer S4Vectors]; };
dmrseq = derive2 { name="dmrseq"; version="1.18.1"; sha256="0djd2r0xzjcyw496wdw2gwzk4wjf3jp639b198x4pc0g0mmgw245"; depends=[AnnotationHub annotatr BiocParallel bsseq bumphunter DelayedMatrixStats GenomeInfoDb GenomicRanges ggplot2 IRanges locfit matrixStats nlme outliers RColorBrewer rtracklayer S4Vectors]; };
doppelgangR = derive2 { name="doppelgangR"; version="1.26.0"; sha256="1qfgfvxj44zyqfcj57lphrqgh7yb3lv807bl9xhg7k2gc3rmy5n1"; depends=[Biobase BiocParallel digest impute mnormt SummarizedExperiment sva]; };
doseR = derive2 { name="doseR"; version="1.14.0"; sha256="0cpjy8whi7nhpyhyz8k2g70l7rhfpg2xcgclxdasbrj695qy79f0"; depends=[digest edgeR lme4 matrixStats mclust RUnit S4Vectors SummarizedExperiment]; };
dpeak = derive2 { name="dpeak"; version="1.10.0"; sha256="1cnbvi8x3zjfvbsc71gz8pk7x7fglydhnc8msp6c10sd06blpibs"; depends=[BSgenome IRanges MASS Rcpp]; };
@ -1360,7 +1360,7 @@ in with self; {
epialleleR = derive2 { name="epialleleR"; version="1.6.1"; sha256="0b416ibi9y81h7xycj1sxmq344ami3a5mcqac3rzbn3l380kl5ms"; depends=[BH BiocGenerics data_table GenomeInfoDb GenomicRanges Rcpp Rhtslib stringi SummarizedExperiment VariantAnnotation zlibbioc]; };
epidecodeR = derive2 { name="epidecodeR"; version="1.6.0"; sha256="0qfb912xsyp4cvblhpwpa22iziwqz39hfnf8x68d23pnfwnb1v74"; depends=[dplyr EnvStats GenomicRanges ggplot2 ggpubr IRanges rstatix rtracklayer]; };
epigenomix = derive2 { name="epigenomix"; version="1.38.0"; sha256="0vdrnn2qmcy3znz534m5iynvzw208whcyypw7mhdqvrfzkzb4m4a"; depends=[beadarray Biobase BiocGenerics GenomeInfoDb GenomicRanges IRanges MCMCpack Rsamtools S4Vectors SummarizedExperiment]; };
epigraHMM = derive2 { name="epigraHMM"; version="1.6.3"; sha256="1qnh135gzz7fq73ryqg3bax0bw6krghpyf05b9xp5py1fk9ic9d3"; depends=[bamsignals csaw data_table GenomeInfoDb GenomicRanges ggplot2 ggpubr GreyListChIP IRanges limma magrittr MASS Matrix pheatmap Rcpp RcppArmadillo rhdf5 Rhdf5lib Rsamtools rtracklayer S4Vectors scales SummarizedExperiment]; };
epigraHMM = derive2 { name="epigraHMM"; version="1.6.4"; sha256="137qs09idwrc40379dvl3gmy2dcfhmp2x09rzzslkzkh0nj4ikcn"; depends=[bamsignals csaw data_table GenomeInfoDb GenomicRanges ggplot2 ggpubr GreyListChIP IRanges limma magrittr MASS Matrix pheatmap Rcpp RcppArmadillo rhdf5 Rhdf5lib Rsamtools rtracklayer S4Vectors scales SummarizedExperiment]; };
epihet = derive2 { name="epihet"; version="1.13.0"; sha256="1p5sgb438yj6h0fv0v17dhz1pl32vai5zcbmgpgagrd5829a6a7r"; depends=[data_table doParallel foreach GenomicRanges ggplot2 igraph IRanges pheatmap qvalue ReactomePA Rtsne S4Vectors WGCNA]; };
epimutacions = derive2 { name="epimutacions"; version="1.2.0"; sha256="1anpx122fcrwldkv5bz5c1cmf6a7y1ai8pc5wjpch7c0nim4a8xg"; depends=[AnnotationDbi AnnotationHub BiocGenerics BiocParallel biomaRt bumphunter ensembldb epimutacionsData ExperimentHub GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 ggrepel gridExtra Gviz Homo_sapiens IlluminaHumanMethylation450kanno_ilmn12_hg19 IlluminaHumanMethylation450kmanifest IlluminaHumanMethylationEPICanno_ilm10b2_hg19 IlluminaHumanMethylationEPICmanifest IRanges isotree matrixStats minfi purrr reshape2 robustbase rtracklayer S4Vectors SummarizedExperiment tibble TxDb_Hsapiens_UCSC_hg18_knownGene TxDb_Hsapiens_UCSC_hg19_knownGene TxDb_Hsapiens_UCSC_hg38_knownGene]; };
epistack = derive2 { name="epistack"; version="1.4.0"; sha256="06z380js0hgnps8nkfrk2ay7s8fyqbndipavk5ipihbp80yzmgpx"; depends=[BiocGenerics GenomicRanges IRanges plotrix S4Vectors SummarizedExperiment viridisLite]; };
@ -1378,7 +1378,7 @@ in with self; {
eudysbiome = derive2 { name="eudysbiome"; version="1.28.0"; sha256="0q6x3nlvarhgc1fq5j4h7hxq5dcmfm0fgm3lmgz63bcbpsf60n5g"; depends=[Biostrings plyr R_utils Rsamtools]; };
evaluomeR = derive2 { name="evaluomeR"; version="1.14.0"; sha256="0wjmm2wzqprn0v0vn90cc3b3wsa274b305p661fdpsql4714jmrq"; depends=[class cluster corrplot flexmix fpc ggdendro ggplot2 kableExtra MASS matrixStats mclust MultiAssayExperiment plotrix prabclus randomForest Rdpack reshape2 SummarizedExperiment]; };
exomeCopy = derive2 { name="exomeCopy"; version="1.44.0"; sha256="11a95rpqzc5502s75ar703bv9hisgfx7yqdf03n0q1qh6ykil35g"; depends=[GenomeInfoDb GenomicRanges IRanges Rsamtools]; };
exomePeak2 = derive2 { name="exomePeak2"; version="1.10.0"; sha256="1j8l3q5bq3yb1889vjpk8l9qzrmg7lv38m7jb57cb9q67sflqjzs"; depends=[BiocGenerics BiocParallel Biostrings BSgenome DESeq2 GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 IRanges magrittr mclust Rsamtools rtracklayer S4Vectors speedglm SummarizedExperiment]; };
exomePeak2 = derive2 { name="exomePeak2"; version="1.10.0"; sha256="1j8l3q5bq3yb1889vjpk8l9qzrmg7lv38m7jb57cb9q67sflqjzs"; depends=[BiocGenerics BiocParallel Biostrings BSgenome DESeq2 GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 IRanges magrittr mclust Rsamtools rtracklayer S4Vectors SummarizedExperiment]; };
extraChIPs = derive2 { name="extraChIPs"; version="1.2.4"; sha256="1jhpzw7ps8bknf3b1pjcpsf5kncm3ia7q5niygvrw3idkbszz2c2"; depends=[BiocIO BiocParallel broom ComplexUpset csaw dplyr edgeR EnrichedHeatmap forcats GenomeInfoDb GenomicInteractions GenomicRanges ggforce ggplot2 ggrepel ggside glue Gviz InteractionSet IRanges limma patchwork RColorBrewer rlang Rsamtools rtracklayer S4Vectors scales stringr SummarizedExperiment tibble tidyr tidyselect vctrs VennDiagram]; };
fCCAC = derive2 { name="fCCAC"; version="1.24.0"; sha256="1r4rdbv1xv8rwsna8w89fzd76hzspf825fxzcn475ll31gmsxsrv"; depends=[ComplexHeatmap fda genomation GenomicRanges ggplot2 IRanges RColorBrewer S4Vectors]; };
fCI = derive2 { name="fCI"; version="1.28.0"; sha256="1jiws5q3ppq0z0s71nhb6fs63470v2di45y0gdf7anjnpxgjcjq9"; depends=[FNN gtools psych rgl VennDiagram zoo]; };
@ -1405,7 +1405,7 @@ in with self; {
flowCHIC = derive2 { name="flowCHIC"; version="1.32.0"; sha256="18mcywl4857wmka63rcnvp2xvh8wj5r8gvbsri9a3f4190wg8yn9"; depends=[EBImage flowCore ggplot2 hexbin vegan]; };
flowCL = derive2 { name="flowCL"; version="1.35.0"; sha256="1jxr0zn3fgm5nqishssxh332mmxfz3fc9zgshn0lbq4avxc2x128"; depends=[graph Rgraphviz]; };
flowClean = derive2 { name="flowClean"; version="1.36.0"; sha256="1wqwq8fw0dk78l43p4cjzll3psc0d4mg7gjckddvpmzlg6w4ha3k"; depends=[bit changepoint flowCore sfsmisc]; };
flowClust = derive2 { name="flowClust"; version="3.36.0"; sha256="1l1lfgm6x06gyzda36m6gvqmb91zbrz8m83b1fnfzpxkhqha20yq"; depends=[Biobase BiocGenerics flowCore graph]; };
flowClust = derive2 { name="flowClust"; version="3.36.1"; sha256="1r27nm5dxlhl5rk96dkjfx8326bvdgx55xg4w2zji3m49x9db2gs"; depends=[Biobase BiocGenerics flowCore graph]; };
flowCore = derive2 { name="flowCore"; version="2.10.0"; sha256="0j0ryyz3vcih964is5gdm2jp39ssdli9q6r03q6rj9nwzplq5asj"; depends=[BH Biobase BiocGenerics cpp11 cytolib matrixStats Rcpp RProtoBufLib S4Vectors]; };
flowCut = derive2 { name="flowCut"; version="1.8.0"; sha256="0p66wcr940m5nvl024izqn3w0x6zmp0n7j43xj70arfcxrxp9gxd"; depends=[Cairo e1071 flowCore flowDensity]; };
flowCyBar = derive2 { name="flowCyBar"; version="1.34.0"; sha256="1nbg49s18mxvr5pzv4lx4hvdrwxn5spagxn71zid5kgk13f142a6"; depends=[gplots vegan]; };
@ -1442,7 +1442,7 @@ in with self; {
gcapc = derive2 { name="gcapc"; version="1.22.0"; sha256="1n3g6fvj86q9n6q3ccmj6ns0gdd4sqfdm43sh1hpxkid9v88209y"; depends=[BiocGenerics Biostrings BSgenome GenomeInfoDb GenomicAlignments GenomicRanges IRanges MASS matrixStats Rsamtools S4Vectors]; };
gcatest = derive2 { name="gcatest"; version="1.28.2"; sha256="1f2bp16x7ji9sh5kk150w57gqpbrisrb0xlkjv8wnd63j0vnng3l"; depends=[lfa]; };
gcrma = derive2 { name="gcrma"; version="2.70.0"; sha256="0a3wjwjgjkpmfvgg0b4jc1rkwzsqrjbaziydjfnkll4rw9xcavy1"; depends=[affy affyio Biobase BiocManager Biostrings XVector]; };
gdsfmt = derive2 { name="gdsfmt"; version="1.34.0"; sha256="1ck3qq4vhjp6vvicpldr7d2rkpspp5albjkbqjbshnbq11fhrk06"; depends=[]; };
gdsfmt = derive2 { name="gdsfmt"; version="1.34.1"; sha256="1sx7yw44djrnc6km8fip3w3vclkgz5s0w6ibp8lpvmjcay8nv2sx"; depends=[]; };
geNetClassifier = derive2 { name="geNetClassifier"; version="1.38.0"; sha256="1ahlml1ssjmg126ki1phdprq4v0nawzbbfq8jray5ypaj32qx3r2"; depends=[Biobase e1071 EBarrays minet]; };
gemini = derive2 { name="gemini"; version="1.12.0"; sha256="12p44p3nzn32am2m609k64iy4lfj42dygdxmb770ld8lpihhrkmz"; depends=[dplyr ggplot2 magrittr mixtools pbmcapply scales]; };
gemma_R = derive2 { name="gemma.R"; version="1.0.1"; sha256="0m6mmv55ghvwqw462ym335bcng61c52d84irkn5xwq6yzr2dgxsa"; depends=[Biobase bit64 data_table glue httr jsonlite lubridate magrittr memoise rappdirs rlang S4Vectors stringr SummarizedExperiment tibble tidyr]; };
@ -1479,7 +1479,7 @@ in with self; {
glmGamPoi = derive2 { name="glmGamPoi"; version="1.10.2"; sha256="1ihjqzdhx6k99gdd4556xxn9822sblg6vmblcmbzml01bhv6xzar"; depends=[beachmat BiocGenerics DelayedArray DelayedMatrixStats HDF5Array MatrixGenerics matrixStats Rcpp RcppArmadillo rlang SingleCellExperiment SummarizedExperiment]; };
glmSparseNet = derive2 { name="glmSparseNet"; version="1.16.0"; sha256="1573cclc2qn4mhw24k7ab75a9inc7z205b0j85favmvv1zcyqal4"; depends=[biomaRt digest dplyr forcats futile_logger futile_options ggplot2 glmnet glue httr Matrix MultiAssayExperiment readr reshape2 stringr SummarizedExperiment survminer]; };
globalSeq = derive2 { name="globalSeq"; version="1.26.0"; sha256="0l4n755v8gxxrxqgzhks4yz06rr3m703zaaavh0fyryk2mnijpip"; depends=[]; };
globaltest = derive2 { name="globaltest"; version="5.52.0"; sha256="1qcrs7dasb1aaws3zkiipznlc1z6i7zijhcsfv6hw3d9wpb0np9k"; depends=[annotate AnnotationDbi Biobase survival]; };
globaltest = derive2 { name="globaltest"; version="5.52.1"; sha256="1g5dv3bw0fj8sq0hsr8c7nh6n1rzvx1bisqlyqjqq3f8lsyb51kb"; depends=[annotate AnnotationDbi Biobase survival]; };
gmapR = derive2 { name="gmapR"; version="1.40.0"; sha256="03fi4ld4f102xch75z6s67kb27mvyg5zik5n59ni4zdiipi9i2cl"; depends=[Biobase BiocGenerics BiocParallel Biostrings BSgenome GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges Rsamtools rtracklayer S4Vectors VariantAnnotation]; };
gmoviz = derive2 { name="gmoviz"; version="1.10.0"; sha256="0vafsa3i8z08bfl4x0adlg3bf0jdw4a7zb459cw7bfdkkw8g4850"; depends=[BiocGenerics Biostrings circlize colorspace ComplexHeatmap GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges gridBase IRanges pracma Rsamtools rtracklayer S4Vectors]; };
goProfiles = derive2 { name="goProfiles"; version="1.60.0"; sha256="0wkvb79lb309ff6iv8p23z9rwrrv7qha86ngs0ag670mpm9yra5j"; depends=[AnnotationDbi Biobase CompQuadForm GO_db stringr]; };
@ -1531,7 +1531,7 @@ in with self; {
iSEE = derive2 { name="iSEE"; version="2.10.0"; sha256="1l2bwqk7ivj79xxjzc0hc3x5v5h19zpk9pa0vbpb5p64z1pshnjn"; depends=[BiocGenerics circlize colourpicker ComplexHeatmap DT ggplot2 ggrepel igraph mgcv rintrojs S4Vectors shiny shinyAce shinydashboard shinyjs shinyWidgets SingleCellExperiment SummarizedExperiment vipor viridisLite]; };
iSEEhex = derive2 { name="iSEEhex"; version="1.0.0"; sha256="06n9ls71rg2kilr3kjlwwk5rnj8v68svjmzcr2hg0gwwyaxcyk9w"; depends=[ggplot2 hexbin iSEE shiny SummarizedExperiment]; };
iSEEhub = derive2 { name="iSEEhub"; version="1.0.0"; sha256="1ggkm7931axcl0464h0d5cnf5lbd6nx3fbac1zrlkwyb2lym7wi8"; depends=[AnnotationHub BiocManager DT ExperimentHub iSEE rintrojs S4Vectors shiny shinydashboard shinyjs SingleCellExperiment SummarizedExperiment]; };
iSEEu = derive2 { name="iSEEu"; version="1.10.0"; sha256="0040k9p1bmlg2065s3a124qvx5qgqqs4kgbkkz0k9vsdvr3z87zs"; depends=[colourpicker DT ggplot2 IRanges iSEE iSEEhex S4Vectors shiny shinyAce SingleCellExperiment SummarizedExperiment]; };
iSEEu = derive2 { name="iSEEu"; version="1.10.1"; sha256="04c2ha4s4fvk30qm65shzzvymiilj0y85qdjc3lw4c90jfvnf44q"; depends=[colourpicker DT ggplot2 IRanges iSEE iSEEhex S4Vectors shiny shinyAce SingleCellExperiment SummarizedExperiment]; };
iSeq = derive2 { name="iSeq"; version="1.50.0"; sha256="1h0da0298g2lvvqbys3jh2acjjzh1dvivfpl07g319nafxkfsi1q"; depends=[]; };
iasva = derive2 { name="iasva"; version="1.16.0"; sha256="192cpnpyyjf16pqnzj70nsqkzv6wp4acia7fciz1zvz5jhncrsva"; depends=[BiocParallel cluster irlba SummarizedExperiment]; };
ibh = derive2 { name="ibh"; version="1.46.0"; sha256="0kxqpb9711yxg5xz2mhpwjw9nwixmfzzy6qql1sifi4mp6bh2fzf"; depends=[simpIntLists]; };
@ -1672,7 +1672,7 @@ in with self; {
minfi = derive2 { name="minfi"; version="1.44.0"; sha256="15989zilgy2j4k4nw046qg8wli7ynjh2b1yzfv7cwgn87mp618lc"; 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="1.28.0"; sha256="0662jsrw745973kf3f95l3n6i5s9h2nk2ap6alv8sb5rkykva2in"; depends=[AnnotationDbi ggplot2 graph org_Hs_eg_db Rgraphviz ROntoTools]; };
mirTarRnaSeq = derive2 { name="mirTarRnaSeq"; version="1.6.0"; sha256="07lfh8c7ks9lbnskvqjhjrssp0wk1kpp7mbh7c7cg6q1kxcxpqyx"; depends=[assertthat caTools corrplot data_table dplyr ggplot2 MASS pheatmap pscl purrr R_utils reshape2]; };
missMethyl = derive2 { name="missMethyl"; version="1.32.0"; sha256="10r3yvamkd1h291lmbas66mshrmy7djkz6pldh8lpqngm0rpgdr6"; depends=[AnnotationDbi BiasedUrn Biobase BiocGenerics GenomicRanges GO_db IlluminaHumanMethylation450kanno_ilmn12_hg19 IlluminaHumanMethylation450kmanifest IlluminaHumanMethylationEPICanno_ilm10b4_hg19 IlluminaHumanMethylationEPICmanifest IRanges limma methylumi minfi org_Hs_eg_db ruv S4Vectors statmod stringr SummarizedExperiment]; };
missMethyl = derive2 { name="missMethyl"; version="1.32.1"; sha256="1rrm8m68kgjkrw1wdli5lrwqlavhbm490zgnj5vafzpvx7xajfma"; depends=[AnnotationDbi BiasedUrn Biobase BiocGenerics GenomicRanges GO_db IlluminaHumanMethylation450kanno_ilmn12_hg19 IlluminaHumanMethylation450kmanifest IlluminaHumanMethylationEPICanno_ilm10b4_hg19 IlluminaHumanMethylationEPICmanifest IRanges limma methylumi minfi org_Hs_eg_db ruv S4Vectors statmod stringr SummarizedExperiment]; };
missRows = derive2 { name="missRows"; version="1.18.0"; sha256="0kwbmhz80an07fcp6skv4bik0ncszxcllfi7jv9h0k814qciij0y"; depends=[ggplot2 gtools MultiAssayExperiment plyr S4Vectors]; };
mistyR = derive2 { name="mistyR"; version="1.6.1"; sha256="0kcqcr1bmmhxngmygr64ca5kl8gsc7z9qwq2ivcc97f78xs3p6p8"; depends=[assertthat caret deldir digest distances dplyr filelock furrr ggplot2 purrr R_utils ranger readr ridge rlang rlist stringr tibble tidyr tidyselect withr]; };
mitch = derive2 { name="mitch"; version="1.10.0"; sha256="174hiq8xzbvdkfxdgm742sjs7qcmnkb9shcid1p8x8ci6fk9vs61"; depends=[beeswarm echarts4r GGally ggplot2 gplots gridExtra knitr MASS plyr reshape2 rmarkdown]; };
@ -1694,12 +1694,12 @@ in with self; {
msPurity = derive2 { name="msPurity"; version="1.24.0"; sha256="1w998i5lv1c2485cmdzk31inykhl64s7njaj725cs1r3gzi4l7h4"; depends=[DBI dbplyr doSNOW dplyr fastcluster foreach ggplot2 magrittr mzR plyr Rcpp reshape2 RSQLite stringr]; };
msa = derive2 { name="msa"; version="1.30.1"; sha256="064hmry0zhmpchxgjsw0krsybr9v9gbsz26zmj2a39pg1nggwbq4"; depends=[BiocGenerics Biostrings IRanges Rcpp S4Vectors]; };
msgbsR = derive2 { name="msgbsR"; version="1.22.0"; sha256="0g6d0gx5af61svxjdzx438vz24sd81qml7f755kq8nrr89pacvh0"; depends=[BSgenome easyRNASeq edgeR GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggbio ggplot2 IRanges plyr R_utils Rsamtools S4Vectors SummarizedExperiment]; };
mslp = derive2 { name="mslp"; version="1.0.1"; sha256="01w9lzfl1vci4z63yzcjk9fn7yzkcxiw6ms528qbg3nmfq08kx5a"; depends=[data_table doRNG fmsb foreach magrittr org_Hs_eg_db pROC randomForest RankProd]; };
mslp = derive2 { name="mslp"; version="1.0.2"; sha256="0sv6a9vjrgi4cd2mvb88jvr8wdwf6hr3570zpq3w3072m8m8gj4v"; depends=[data_table doRNG fmsb foreach magrittr org_Hs_eg_db pROC randomForest RankProd]; };
msmsEDA = derive2 { name="msmsEDA"; version="1.36.0"; sha256="17xklsg483zd205q5hyxy6b3cgrb53pplb1wc7pmv5638y7nsq2v"; depends=[gplots MASS MSnbase RColorBrewer]; };
msmsTests = derive2 { name="msmsTests"; version="1.36.0"; sha256="10frsvqhi3i0v2w4q4q9xz1ykyf6s3nrjlmn94x3kd06p3s839k3"; depends=[edgeR msmsEDA MSnbase qvalue]; };
msqrob2 = derive2 { name="msqrob2"; version="1.6.1"; sha256="1cv7i2n8a470jzpldlwyrx12d8my2al2522vilyyfr9j74xgi0ln"; depends=[BiocParallel codetools limma lme4 MASS Matrix MultiAssayExperiment purrr QFeatures SummarizedExperiment]; };
multiClust = derive2 { name="multiClust"; version="1.28.0"; sha256="0mw48jm154c0k9nhal56xc4jv0n3ms0s1770g2i2lxkr37905swq"; depends=[amap cluster ctc dendextend mclust survival]; };
multiGSEA = derive2 { name="multiGSEA"; version="1.8.1"; sha256="1y43nf7c3zyqjsdpx7g5xfdy53qwzzbynb9lhhyj6rbbirrpj48b"; depends=[AnnotationDbi dplyr fgsea graphite magrittr metap rappdirs rlang]; };
multiGSEA = derive2 { name="multiGSEA"; version="1.8.2"; sha256="1s8rdrzpvnscdisv1ld31aiv5vbddvr7f523sc9ngv2nsmisxdq8"; depends=[AnnotationDbi dplyr fgsea graphite magrittr metap rappdirs rlang]; };
multiHiCcompare = derive2 { name="multiHiCcompare"; version="1.16.0"; sha256="0mwb61c6yqq1frnsgp3nafmlrl1zi8sxckp5yw7z083805y3fbyr"; depends=[aggregation BiocParallel data_table dplyr edgeR GenomeInfoDb GenomeInfoDbData GenomicRanges HiCcompare pbapply pheatmap qqman]; };
multiMiR = derive2 { name="multiMiR"; version="1.20.0"; sha256="1zfjr1cw1qpi70wxrkw32y3dmwhbsdzd2522cgkj4x97g4d5cn99"; depends=[AnnotationDbi BiocGenerics dplyr purrr RCurl tibble XML]; };
multiOmicsViz = derive2 { name="multiOmicsViz"; version="1.22.0"; sha256="0g28ksb9vf2lpv15s9s64nnz6smhxrf9cbsw4kba0dlyrrzzha4a"; depends=[doParallel foreach SummarizedExperiment]; };
@ -1742,7 +1742,7 @@ in with self; {
nuCpos = derive2 { name="nuCpos"; version="1.16.3"; sha256="14anlg6a7b3qw2k39q273p5396v3nqlask0gz92h170z24gjyc1s"; depends=[]; };
nucleR = derive2 { name="nucleR"; version="2.30.0"; sha256="0j8g0lf6pzqzak259fp6xckgcjrabqgd28bwy9fbx3pd1qj5yrh0"; depends=[Biobase BiocGenerics Biostrings dplyr GenomeInfoDb GenomicRanges ggplot2 IRanges magrittr Rsamtools S4Vectors ShortRead]; };
nucleoSim = derive2 { name="nucleoSim"; version="1.26.0"; sha256="0cgljwk9car3s5ncslx0j0bya6hchfv1zk09q8r0y6258mim4qy6"; depends=[IRanges S4Vectors]; };
nullranges = derive2 { name="nullranges"; version="1.4.0"; sha256="01f7x99nzgi0si02p5bsjvf0mybl52kxnkm2j1f1s2rai5srkca4"; depends=[data_table GenomeInfoDb GenomicRanges ggplot2 ggridges InteractionSet IRanges ks plyranges progress rlang S4Vectors scales speedglm]; };
nullranges = derive2 { name="nullranges"; version="1.4.0"; sha256="01f7x99nzgi0si02p5bsjvf0mybl52kxnkm2j1f1s2rai5srkca4"; depends=[data_table GenomeInfoDb GenomicRanges ggplot2 ggridges InteractionSet IRanges ks plyranges progress rlang S4Vectors scales]; };
occugene = derive2 { name="occugene"; version="1.58.0"; sha256="13hv71w25jzlf0fs5wx400m1zh4l4vxlvv42vidiyggj894ky5a3"; depends=[]; };
octad = derive2 { name="octad"; version="1.0.0"; sha256="0qa407rhi9z1n2hif40j27vbfsy222wi2hh26qn4s0s7f2fnfyfl"; depends=[AnnotationHub Biobase data_table DESeq2 dplyr EDASeq edgeR ExperimentHub foreach ggplot2 GSVA htmlwidgets httr limma magrittr octad_db plotly reshape2 Rfast rhdf5 RUVSeq S4Vectors]; };
odseq = derive2 { name="odseq"; version="1.26.0"; sha256="0p51lay3xasqg55j99gdx1gpk93p4m2czvbw912h559v2s4hnzqq"; depends=[kebabs mclust msa]; };
@ -1799,6 +1799,7 @@ in with self; {
periodicDNA = derive2 { name="periodicDNA"; version="1.8.0"; sha256="03wdxbgsrj2c7j3fgxigjbq349y5c8cw80xvb5ja7lbi1isfb785"; depends=[BiocParallel Biostrings BSgenome cowplot GenomeInfoDb GenomicRanges ggplot2 IRanges magrittr rtracklayer S4Vectors zoo]; };
pgca = derive2 { name="pgca"; version="1.22.0"; sha256="0bcq1qks87jjgd2bwpds6xvcvidcvl9pq53mi0dafihgd0s2ycfn"; depends=[]; };
phantasus = derive2 { name="phantasus"; version="1.18.4"; sha256="0rjn66xjkr57w4nsjczxrw3hw90r9zfwqbmhs8pw4y1hd7j1alhi"; depends=[AnnotationDbi assertthat Biobase ccaPP curl data_table DESeq2 fgsea GEOquery ggplot2 gtable htmltools httpuv httr jsonlite limma Matrix opencpu pheatmap protolite rhdf5 Rook scales stringr svglite]; };
phemd = derive2 { name="phemd"; version="1.14.1"; sha256="18i2qps2r8h9fqln9gm0wz373xg3lfkgb3my8wk4w944h3an6280"; depends=[Biobase BiocGenerics cluster cowplot destiny ggplot2 igraph maptree monocle phateR pheatmap pracma RANN RColorBrewer reticulate Rtsne S4Vectors scatterplot3d Seurat SingleCellExperiment SummarizedExperiment transport VGAM]; };
phenoTest = derive2 { name="phenoTest"; version="1.46.0"; sha256="0rcgbnqglfs9asyrssnhy7h99kikmnr7s1827y8q2agq3pl96q13"; depends=[annotate AnnotationDbi Biobase biomaRt BMA Category ellipse genefilter ggplot2 gplots GSEABase Heatplus hgu133a_db Hmisc hopach limma mgcv survival xtable]; };
phenomis = derive2 { name="phenomis"; version="1.0.2"; sha256="15lk3wapaaqqrlp02b2cvdlx8dgcvc3vjsfv8i70qh89rljialf8"; depends=[Biobase biodb biodbChebi data_table futile_logger ggplot2 ggrepel htmlwidgets igraph limma MultiAssayExperiment MultiDataSet plotly PMCMRplus ranger RColorBrewer ropls SummarizedExperiment tibble tidyr VennDiagram]; };
phenopath = derive2 { name="phenopath"; version="1.22.0"; sha256="0p2lh858ykhqz0zj4h1vmjd27szwkrlswanapz4shhmvb4plrlbv"; depends=[dplyr ggplot2 Rcpp SummarizedExperiment tibble tidyr]; };
@ -1832,7 +1833,7 @@ in with self; {
primirTSS = derive2 { name="primirTSS"; version="1.16.0"; sha256="00h9m37ga3wsbcafg4c338457xqjlmgmhhkcrvm38x39h20kxrqy"; depends=[BiocGenerics Biostrings BSgenome_Hsapiens_UCSC_hg38 dplyr GenomicRanges GenomicScores Gviz IRanges JASPAR2018 phastCons100way_UCSC_hg38 purrr R_utils rtracklayer S4Vectors shiny stringr TFBSTools tibble tidyr]; };
proActiv = derive2 { name="proActiv"; version="1.8.0"; sha256="150n6nglbji1510g6kkq6b7i0nix70c6zahdrr4a6p1dpg15gfgv"; depends=[AnnotationDbi BiocParallel data_table DESeq2 dplyr GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 gplots IRanges rlang S4Vectors scales SummarizedExperiment tibble]; };
proBAMr = derive2 { name="proBAMr"; version="1.32.0"; sha256="1pn48pmiz6cgc3hjczhpzgld69my7xk37d1k7k37gm0dwzpd85c3"; depends=[AnnotationDbi Biostrings GenomicFeatures GenomicRanges IRanges rtracklayer]; };
proBatch = derive2 { name="proBatch"; version="1.13.0"; sha256="1z55rbgjzxkj0i9gwwbh3wa82w9xflnipkkx58bgnni1nfnbia9k"; depends=[Biobase corrplot data_table dplyr ggfortify ggplot2 lazyeval lubridate magrittr pheatmap preprocessCore purrr pvca RColorBrewer reshape2 rlang scales sva tibble tidyr viridis wesanderson WGCNA]; };
proBatch = derive2 { name="proBatch"; version="1.14.0"; sha256="079dh61v1dmsasrh5sn6sn1rgi34mavxa1sc1y8x6wqjwabm4w1j"; depends=[Biobase corrplot data_table dplyr ggfortify ggplot2 lazyeval lubridate magrittr pheatmap preprocessCore purrr pvca RColorBrewer reshape2 rlang scales sva tibble tidyr viridis wesanderson WGCNA]; };
proDA = derive2 { name="proDA"; version="1.12.0"; sha256="1b1p8sh80x5967rakyq75cj0sz01303w7p05b9irfr69yvfvlj45"; depends=[BiocGenerics extraDistr S4Vectors SummarizedExperiment]; };
proFIA = derive2 { name="proFIA"; version="1.23.0"; sha256="0y08vj401f45dvgxjwjx94hvd0rk1wljk8n1irpkdafg24gv4fvj"; depends=[Biobase BiocParallel minpack_lm missForest pracma ropls xcms]; };
procoil = derive2 { name="procoil"; version="2.26.0"; sha256="1ncls2bgdaaq1kc728p5ay95ypm5byyhpzjck34hfpq867lp7x7m"; depends=[Biostrings kebabs S4Vectors]; };
@ -1851,7 +1852,7 @@ in with self; {
pvca = derive2 { name="pvca"; version="1.38.0"; sha256="1cpyxgw1ynq3dms5yvcwaqd3s55ky80dgy811nl226mji278v9cl"; depends=[Biobase lme4 Matrix vsn]; };
pwOmics = derive2 { name="pwOmics"; version="1.30.0"; sha256="1mklwy9p6miwzvcjzin5q0qcg9625bmbj5hi9dvm6cq48r0x5gwp"; depends=[AnnotationDbi AnnotationHub Biobase BiocGenerics biomaRt data_table GenomicRanges gplots graph igraph rBiopaxParser STRINGdb]; };
pwrEWAS = derive2 { name="pwrEWAS"; version="1.12.0"; sha256="1y8knyl0axnbidkg1z9n1dmchdb79ixr7d6m1g2zhlzp10kmi4pk"; depends=[abind BiocManager CpGassoc doParallel doSNOW foreach genefilter ggplot2 limma pwrEWAS_data shiny shinyBS shinyWidgets truncnorm]; };
qPLEXanalyzer = derive2 { name="qPLEXanalyzer"; version="1.16.0"; sha256="18hswwff9smiz9dr28mmh7fh58wknb8cfzxvg5xdw4fw09cb48m9"; depends=[assertthat Biobase BiocGenerics Biostrings dplyr ggdendro ggplot2 IRanges limma magrittr MSnbase preprocessCore purrr RColorBrewer readr rlang scales stringr tibble tidyr tidyselect]; };
qPLEXanalyzer = derive2 { name="qPLEXanalyzer"; version="1.16.1"; sha256="0jzk0h6lll7yxmiplrk0rhx5pvhq8jjifhi2fj4nyskx1brsnnfh"; depends=[assertthat Biobase BiocGenerics Biostrings dplyr ggdendro ggplot2 IRanges limma magrittr MSnbase preprocessCore purrr RColorBrewer readr rlang scales stringr tibble tidyr tidyselect]; };
qckitfastq = derive2 { name="qckitfastq"; version="1.14.0"; sha256="0220r27adgm8mj348602hzgrbj8f94d0xbcrfg9r5sjaajqbmf8w"; depends=[data_table dplyr ggplot2 magrittr Rcpp reshape2 rlang RSeqAn seqTools zlibbioc]; };
qcmetrics = derive2 { name="qcmetrics"; version="1.36.0"; sha256="1ab6w3ghalgjarkq91ci85dwpwp1dqdsj2m9adlmx05wpljg9qc4"; depends=[Biobase knitr pander S4Vectors xtable]; };
qmtools = derive2 { name="qmtools"; version="1.2.0"; sha256="19zn0q493vn45wllzbzqfgnazr5x6ik2hvh7pay3s95421vls1bd"; depends=[ggplot2 heatmaply igraph MsCoreUtils patchwork rlang scales SummarizedExperiment VIM]; };
@ -1878,7 +1879,7 @@ in with self; {
rScudo = derive2 { name="rScudo"; version="1.14.0"; sha256="1bk7w1rb87j6c3280r6bwnvfhfzdv0ck9g96y0a8k1g297gvyvcc"; depends=[Biobase BiocGenerics igraph S4Vectors stringr SummarizedExperiment]; };
rTRM = derive2 { name="rTRM"; version="1.36.0"; sha256="11dp7vz1343hmaa7lly5m9h9fx94cpqqhsrvbb6vy57bh8nb6v4v"; depends=[AnnotationDbi DBI igraph RSQLite]; };
rTRMui = derive2 { name="rTRMui"; version="1.36.0"; sha256="1gindmnq5vkapmfjpy9hglbk79g0s1sgzdljmhn3m5925h2al4k0"; depends=[MotifDb org_Hs_eg_db org_Mm_eg_db rTRM shiny]; };
rWikiPathways = derive2 { name="rWikiPathways"; version="1.18.0"; sha256="0vk6j07xxkpdaybsiip41xavsiwc8qr165sxab5fy1r13w3ya4d3"; depends=[data_table httr RCurl rjson tidyr XML]; };
rWikiPathways = derive2 { name="rWikiPathways"; version="1.18.1"; sha256="1zh6yz49s4jdpgg17dkkjv32fkp4zvdrcljfpbysbvc9lplrlj65"; depends=[data_table httr RCurl rjson tidyr XML]; };
rain = derive2 { name="rain"; version="1.32.0"; sha256="0zlb52z0wk6057ph12lj7313bfkpbn502568cgdwify8s6q9g8ms"; depends=[gmp multtest]; };
rama = derive2 { name="rama"; version="1.72.0"; sha256="0i6crxnzhwxnc55xh2rv36jfwh4bd30alw1f05ixdrxwqwsslbpy"; depends=[]; };
ramr = derive2 { name="ramr"; version="1.6.0"; sha256="1rn5jvrcl3823124iwwbrjx89yyp3yflhlvjwnf6jldvm5bwqwpz"; depends=[BiocGenerics doParallel doRNG EnvStats ExtDist foreach GenomicRanges ggplot2 IRanges matrixStats reshape2 S4Vectors]; };
@ -1893,7 +1894,7 @@ in with self; {
reconsi = derive2 { name="reconsi"; version="1.10.0"; sha256="1hzwjmnbkdb4v8nvsk06vmyh5hm1snjn1a2q21jingppjs0dzvik"; depends=[ggplot2 ks Matrix matrixStats phyloseq reshape2]; };
recount = derive2 { name="recount"; version="1.24.1"; sha256="0ryxz7kf52rwwri1bbpfpn67ivcx3fxrnym430d4nv6j1qfb1kh4"; depends=[BiocParallel derfinder downloader GenomeInfoDb GenomicRanges GEOquery IRanges RCurl rentrez rtracklayer S4Vectors SummarizedExperiment]; };
recount3 = derive2 { name="recount3"; version="1.8.0"; sha256="1syfy713ybsl8vlvfag6i85icv34k1y0f6g6v168snc2z1xq4yrd"; depends=[BiocFileCache data_table GenomicRanges Matrix R_utils RCurl rtracklayer S4Vectors sessioninfo SummarizedExperiment]; };
recountmethylation = derive2 { name="recountmethylation"; version="1.8.3"; sha256="04xcj58wdsbz4ibx030br2d27lvld4aqvj1j7686r7jcjj2s92kq"; depends=[BiocFileCache HDF5Array IlluminaHumanMethylation450kmanifest minfi R_utils RCurl rhdf5 S4Vectors]; };
recountmethylation = derive2 { name="recountmethylation"; version="1.8.6"; sha256="1nrav24pq3jwi9jmy7b0h799q6bnw1sjd8a0gca3c1pn9zvg8xqn"; depends=[basilisk BiocFileCache DelayedMatrixStats HDF5Array minfi R_utils RCurl reticulate rhdf5 S4Vectors]; };
recoup = derive2 { name="recoup"; version="1.26.0"; sha256="00ia9a9kqmcn329pvipaz15xfci6rw4377hpf7gnxhjkxx4b1rna"; depends=[BiocGenerics biomaRt Biostrings circlize ComplexHeatmap GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 httr IRanges Rsamtools RSQLite rtracklayer S4Vectors stringr]; };
regionReport = derive2 { name="regionReport"; version="1.32.0"; sha256="0ilqm51dnhv5bhda7ljdn1x4hwr4infpngsvwn7wvssvsgp1pcz0"; depends=[BiocStyle DEFormats derfinder DESeq2 GenomeInfoDb GenomicRanges knitr knitrBootstrap RefManageR rmarkdown S4Vectors SummarizedExperiment]; };
regioneR = derive2 { name="regioneR"; version="1.30.0"; sha256="01anwhz0axdl0g2zsaqz1qdxswxrryarbw6pmn5kmlpz4ipiq049"; depends=[Biostrings BSgenome GenomeInfoDb GenomicRanges IRanges memoise rtracklayer S4Vectors]; };
@ -1908,7 +1909,7 @@ in with self; {
rgsepd = derive2 { name="rgsepd"; version="1.30.0"; sha256="1bk6i336x2ng1kvgywcs18v6sn47cndahfbpcagl17x77pcna7by"; depends=[AnnotationDbi biomaRt DESeq2 GO_db goseq gplots org_Hs_eg_db SummarizedExperiment]; };
rhdf5 = derive2 { name="rhdf5"; version="2.42.0"; sha256="1vxs227d1295fz8irr6fsv603cw96a801j8njhblvs0cry38d087"; depends=[rhdf5filters Rhdf5lib]; };
rhdf5client = derive2 { name="rhdf5client"; version="1.20.0"; sha256="0wf0mv1kc3gd7vpazdip9253c1727ns9xysqfipg9lf1ydjny1fq"; depends=[DelayedArray httr R6 rjson S4Vectors]; };
rhdf5filters = derive2 { name="rhdf5filters"; version="1.10.0"; sha256="17x2a3122mm3z9qnalw25am2x08cfpm17nwhigabid3ha3d2mgz1"; depends=[Rhdf5lib]; };
rhdf5filters = derive2 { name="rhdf5filters"; version="1.10.1"; sha256="14rkr0fisy7qrvjikpnwxwag79205hdxy6nkpwz501li4fr1rbnp"; depends=[Rhdf5lib]; };
riboSeqR = derive2 { name="riboSeqR"; version="1.32.0"; sha256="0la8kmxxh5jnqsrmmvyhi313bjdbqkiq16hcxar6mgyjhxlsm610"; depends=[abind baySeq GenomeInfoDb GenomicRanges IRanges Rsamtools seqLogo]; };
ribor = derive2 { name="ribor"; version="1.10.0"; sha256="16ikb3815cmwagjjjcv8rmshybpjl0vfc20mpl5xr92dzbnn7jj2"; depends=[dplyr ggplot2 hash rhdf5 rlang S4Vectors tidyr yaml]; };
ribosomeProfilingQC = derive2 { name="ribosomeProfilingQC"; version="1.10.0"; sha256="04r0nhjfm659i5n2351f67dghjm9jrfvcnzbf7ylqgnhym4ibzrn"; depends=[AnnotationDbi BiocGenerics Biostrings BSgenome cluster EDASeq GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggfittext ggplot2 ggrepel IRanges motifStack Rsamtools Rsubread rtracklayer RUVSeq S4Vectors scales XVector]; };
@ -1930,7 +1931,7 @@ in with self; {
rtracklayer = derive2 { name="rtracklayer"; version="1.58.0"; sha256="1qxr0ffmmkbfkbijz7pbks3kvms9k4a5rmma4j9p7ar477fxvlmk"; depends=[BiocGenerics BiocIO Biostrings GenomeInfoDb GenomicAlignments GenomicRanges IRanges RCurl restfulr Rsamtools S4Vectors XML XVector zlibbioc]; };
runibic = derive2 { name="runibic"; version="1.20.0"; sha256="0g7hqgsq7h0338fmlb4ipv1kwiijcrfajhgwchn5akhspvsch269"; depends=[biclust Rcpp SummarizedExperiment testthat]; };
sRACIPE = derive2 { name="sRACIPE"; version="1.14.0"; sha256="079lmgi6az5ri05lvca58msh678r7k1xwk3xhq8iffqh87wy6cmj"; depends=[BiocGenerics ggplot2 gplots gridExtra htmlwidgets MASS RColorBrewer Rcpp reshape2 S4Vectors SummarizedExperiment umap visNetwork]; };
sSNAPPY = derive2 { name="sSNAPPY"; version="1.2.4"; sha256="0ja3hbsfhmwibc8mj4192kcwcp4bj2lish1nsy7kd6hdv28i5nm8"; depends=[BiocParallel dplyr edgeR ggforce ggnewscale ggplot2 ggraph graphite igraph magrittr org_Hs_eg_db pheatmap purrr Rcpp RcppArmadillo reshape2 rlang SummarizedExperiment tibble]; };
sSNAPPY = derive2 { name="sSNAPPY"; version="1.2.5"; sha256="17z0iz6jr0nx14s4d80j94jdk78af4i1zkin24z56fas28sm2ka8"; depends=[BiocParallel dplyr edgeR ggforce ggnewscale ggplot2 ggraph graphite igraph magrittr org_Hs_eg_db pheatmap purrr Rcpp RcppArmadillo reshape2 rlang SummarizedExperiment tibble]; };
sSeq = derive2 { name="sSeq"; version="1.36.0"; sha256="1w0iq7pih9z8662wj2lj1xbg66n752mx4g2q33ck5vwdxg10ry4c"; depends=[caTools RColorBrewer]; };
safe = derive2 { name="safe"; version="3.38.0"; sha256="1gza1liz0y2i6f5nnnwbwl99fjp3cr1aknxiy3rmbjydfq8yxbrw"; depends=[AnnotationDbi Biobase SparseM]; };
sagenhaft = derive2 { name="sagenhaft"; version="1.68.0"; sha256="0hh9gkv07qrlnarrj7h579dhisyq01c5jjl3rvq5w086wfy9154m"; depends=[SparseM]; };
@ -1940,7 +1941,7 @@ in with self; {
sarks = derive2 { name="sarks"; version="1.10.0"; sha256="1f3yypn7dzjq58jnkv3jc0330mddpapzn1wlvq2crjbh161mxaym"; depends=[binom Biostrings cluster IRanges rJava]; };
satuRn = derive2 { name="satuRn"; version="1.6.0"; sha256="1gldcdnpbxc2bgi5sr3g0cgkfx8gx2jmyadnxzm07zcmi724nsyx"; depends=[BiocParallel boot ggplot2 limma locfdr Matrix pbapply SummarizedExperiment]; };
savR = derive2 { name="savR"; version="1.36.0"; sha256="1b7kjgj2r6lgkdnrq91wcwvwb5an0gfdsbyp7j0pvn2byfm4lply"; depends=[ggplot2 gridExtra reshape2 scales XML]; };
scAlign = derive2 { name="scAlign"; version="1.11.0"; sha256="01gy9p07nyx42i0phgc89yhjavpykzgh1mwr11358ddbwz41hxnr"; depends=[FNN ggplot2 irlba purrr Rtsne Seurat SingleCellExperiment tensorflow]; };
scAlign = derive2 { name="scAlign"; version="1.12.0"; sha256="1mlhxwsfrmhysa5mcyx7vf2jn49snf41yb7xqmyi40wilj9h8qlb"; depends=[FNN ggplot2 irlba purrr Rtsne Seurat SingleCellExperiment tensorflow]; };
scAnnotatR = derive2 { name="scAnnotatR"; version="1.4.0"; sha256="0rc035kzbzrxvlcpphzg0yg7q82jvlxpi9xjq8q59hvbpyg1sz93"; depends=[AnnotationHub ape caret data_tree dplyr e1071 ggplot2 kernlab pROC ROCR Seurat SingleCellExperiment SummarizedExperiment]; };
scBFA = derive2 { name="scBFA"; version="1.12.0"; sha256="0884s9laa63yf2p9wf66a67ipkc2x075c432x8p96vr326p4h8nf"; depends=[copula DESeq2 ggplot2 MASS Matrix Seurat SingleCellExperiment SummarizedExperiment zinbwave]; };
scBubbletree = derive2 { name="scBubbletree"; version="1.0.0"; sha256="0ivyp3zf7clr4zbdv2srjv42dx2zvlaq4yprccxb3yimrnmihks6"; depends=[ape future future_apply ggplot2 ggtree patchwork reshape2 scales Seurat]; };
@ -2096,8 +2097,8 @@ in with self; {
ternarynet = derive2 { name="ternarynet"; version="1.42.0"; sha256="01z262509vka2sfhzccwlmgi5frf56x07gbsan762hgvrcscg8jb"; depends=[BiocParallel igraph]; };
terraTCGAdata = derive2 { name="terraTCGAdata"; version="1.2.0"; sha256="1yfvqdsgd3apan43cbjin95mwnbym1m0f1c8x212k277cc3rm22r"; depends=[AnVIL BiocFileCache dplyr GenomicRanges MultiAssayExperiment RaggedExperiment readr S4Vectors TCGAutils tidyr]; };
tidySingleCellExperiment = derive2 { name="tidySingleCellExperiment"; version="1.8.0"; sha256="0kkxd64rlksw7l0hw53ckc9mhsvsb0yj8w078bh4rd16iqk3jnnc"; depends=[cli dplyr ellipsis fansi ggplot2 lifecycle magrittr pillar plotly purrr rlang S4Vectors SingleCellExperiment stringr SummarizedExperiment tibble tidyr tidyselect ttservice]; };
tidySummarizedExperiment = derive2 { name="tidySummarizedExperiment"; version="1.8.0"; sha256="0y7k0svcjx0lvxn3jw8g7vkrvwhvj9b7mhb0igavad1rc5pc54f3"; depends=[cli dplyr ellipsis fansi ggplot2 lifecycle magrittr pillar plotly purrr rlang S4Vectors stringr SummarizedExperiment tibble tidyr tidyselect vctrs]; };
tidybulk = derive2 { name="tidybulk"; version="1.10.0"; sha256="1n31wqad7wdfyfy1mcjsq68rlyyyd15srcrvz6ylp2pi8nbwxfly"; depends=[crayon dplyr GenomicRanges lifecycle magrittr preprocessCore purrr readr rlang S4Vectors scales stringi stringr SummarizedExperiment tibble tidyr tidyselect]; };
tidySummarizedExperiment = derive2 { name="tidySummarizedExperiment"; version="1.8.1"; sha256="1sry782zf2sisjwlhgdh1vfr0ljbw2rrwwb907jxmafg6jm96rxq"; depends=[cli dplyr ellipsis fansi ggplot2 lifecycle magrittr pillar plotly purrr rlang S4Vectors stringr SummarizedExperiment tibble tidyr tidyselect vctrs]; };
tidybulk = derive2 { name="tidybulk"; version="1.10.1"; sha256="100xnjz73wl48a93gv4361pllyb96nbhg5q8spgq131wp0i0zjzz"; depends=[crayon dplyr GenomicRanges lifecycle magrittr preprocessCore purrr readr rlang S4Vectors scales stringi stringr SummarizedExperiment tibble tidyr tidyselect]; };
tigre = derive2 { name="tigre"; version="1.52.0"; sha256="1cj4yqdad1xs8k682qx92b03nbyx51qdqsf7y90bll3z51xhwvdq"; depends=[annotate AnnotationDbi Biobase BiocGenerics DBI gplots RSQLite]; };
tilingArray = derive2 { name="tilingArray"; version="1.76.0"; sha256="19bkgblpkcp3w3sdyn82c37gkz1sv3r4d546zpbnh36q2pi3l4zd"; depends=[affy Biobase genefilter pixmap RColorBrewer strucchange vsn]; };
timeOmics = derive2 { name="timeOmics"; version="1.10.0"; sha256="1szhdd29gfa7ah7yf683d69s2w0w6r8nh3kc7fii3vnyqspspb19"; depends=[dplyr ggplot2 ggrepel lmtest magrittr mixOmics plyr purrr stringr tibble tidyr]; };
@ -2136,11 +2137,11 @@ in with self; {
tximeta = derive2 { name="tximeta"; version="1.16.1"; sha256="15qf8s9akl5qp5wklph5i61d96d9ifr5ijl796v1vafwrj4f3wpa"; depends=[AnnotationDbi AnnotationHub BiocFileCache Biostrings ensembldb GenomeInfoDb GenomicFeatures GenomicRanges IRanges jsonlite Matrix S4Vectors SummarizedExperiment tibble tximport]; };
tximport = derive2 { name="tximport"; version="1.26.1"; sha256="1r67q4nb2bx9nqycyr2gnfmh4gizl0c7l510vmlcdvplv3yi73yn"; depends=[]; };
uSORT = derive2 { name="uSORT"; version="1.24.0"; sha256="1fhhl00qdj7ihvb3ia2nd215m1ylbaszpyq1w7bmgv89v5ghhsgf"; depends=[Biobase BiocGenerics cluster fpc gplots igraph Matrix monocle plyr RANN RSpectra VGAM]; };
uncoverappLib = derive2 { name="uncoverappLib"; version="1.7.0"; sha256="1fsn5wpknx1f6sj12x9q456iqi68kwgcqzkk3343hfg185rnn8sh"; depends=[BiocFileCache BSgenome_Hsapiens_UCSC_hg19 BSgenome_Hsapiens_UCSC_hg38 condformat DT EnsDb_Hsapiens_v75 EnsDb_Hsapiens_v86 GenomicRanges Gviz Homo_sapiens markdown openxlsx org_Hs_eg_db OrganismDbi processx rappdirs rlist Rsamtools S4Vectors shiny shinyBS shinycssloaders shinyjs shinyWidgets stringr TxDb_Hsapiens_UCSC_hg19_knownGene TxDb_Hsapiens_UCSC_hg38_knownGene]; };
uncoverappLib = derive2 { name="uncoverappLib"; version="1.8.1"; sha256="196xw6m69ld6nnbgqyyr7vd9qgqlczybgs7phvm7g36q4rywsnkm"; depends=[BiocFileCache condformat DT EnsDb_Hsapiens_v75 EnsDb_Hsapiens_v86 GenomicRanges Gviz Homo_sapiens markdown openxlsx org_Hs_eg_db OrganismDbi processx rappdirs rlist Rsamtools S4Vectors shiny shinyBS shinycssloaders shinyjs shinyWidgets stringr TxDb_Hsapiens_UCSC_hg19_knownGene TxDb_Hsapiens_UCSC_hg38_knownGene]; };
unifiedWMWqPCR = derive2 { name="unifiedWMWqPCR"; version="1.34.0"; sha256="0zkqr1s8gagwsh33kzp0n2n7ff5jhfn6a60gvab5spk7vr76j442"; depends=[BiocGenerics HTqPCR]; };
universalmotif = derive2 { name="universalmotif"; version="1.16.0"; sha256="1vfg703wxbgxw2cwqqz3kfyqj4za5n3skxxzi8c31azamg4hxs18"; depends=[BiocGenerics Biostrings ggplot2 IRanges MASS Rcpp RcppThread rlang S4Vectors yaml]; };
updateObject = derive2 { name="updateObject"; version="1.2.0"; sha256="13rq1hv0rg8cj3z8d2b9mfih5sybicb4razv8vaic1i7c7sbypwf"; depends=[BiocGenerics digest S4Vectors]; };
variancePartition = derive2 { name="variancePartition"; version="1.28.7"; sha256="0iv5c5p0g4axhanc62mmk0c43qcwdsxzslxh5qdck0v1kb7bd1d9"; depends=[aod Biobase BiocParallel doParallel foreach ggplot2 gplots iterators limma lme4 lmerTest MASS Matrix pbkrtest progress Rdpack remaCor reshape2 RhpcBLASctl rlang scales]; };
variancePartition = derive2 { name="variancePartition"; version="1.28.9"; sha256="1al7wkbv26gldba61gq80c3mznsxwr7z5njv2s0lb7hnll9bscar"; depends=[aod Biobase BiocParallel doParallel foreach ggplot2 gplots iterators limma lme4 lmerTest MASS Matrix pbkrtest progress Rdpack remaCor reshape2 RhpcBLASctl rlang scales]; };
vbmp = derive2 { name="vbmp"; version="1.66.0"; sha256="1gfvk1g9q73p9z91zasblya1w218yhzawp6dgyf0lnldx36kpvc9"; depends=[]; };
velociraptor = derive2 { name="velociraptor"; version="1.8.0"; sha256="07nwx9cahia4a6g15xhccdlwxnhvwq46dy2hqcqqzydgpsapa6wv"; depends=[basilisk BiocGenerics BiocParallel BiocSingular DelayedArray Matrix reticulate S4Vectors scuttle SingleCellExperiment SummarizedExperiment zellkonverter]; };
veloviz = derive2 { name="veloviz"; version="1.4.0"; sha256="01f2d28h0gnh38g50yphmg3aqy1ya2ysj1xabs2a6y3wnqzrahzk"; depends=[igraph Matrix mgcv Rcpp RSpectra]; };
@ -2228,7 +2229,6 @@ in with self; {
methyAnalysis = derive2 { name="methyAnalysis"; version="1.34.0"; sha256="05k3n7iy5ijidbnblbqqas8dsj8drwzbhyrbs8wl1ypkg51havi0"; depends=[annotate AnnotationDbi Biobase BiocGenerics biomaRt genefilter GenomeInfoDb GenomicFeatures GenomicRanges Gviz IRanges lumi methylumi org_Hs_eg_db rtracklayer SummarizedExperiment VariantAnnotation]; broken = true; };
networkBMA = derive2 { name="networkBMA"; version="2.35.0"; sha256="0xa0b977apbr6p9kqk38582af635kp99csj32bsn2bf8pjsmd4d2"; depends=[BH BMA leaps Rcpp RcppArmadillo RcppEigen]; broken = true; };
perturbatr = derive2 { name="perturbatr"; version="1.13.0"; sha256="0ssk8cr42hibn917s2z2nzcdan54c7xiydypbi8f3g4w68q4ly31"; depends=[assertthat diffusr doParallel dplyr foreach formula_tools ggplot2 igraph lazyeval lme4 magrittr rlang scales tibble tidyr]; broken = true; };
phemd = derive2 { name="phemd"; version="1.12.0"; sha256="0nn0qgb0rz4j2xsjq0wydjhg5pmf2ra67rm9fdm4m1izmzwa0nhs"; depends=[Biobase BiocGenerics cluster cowplot destiny ggplot2 igraph maptree monocle phateR pheatmap pracma RANN RColorBrewer reticulate Rtsne S4Vectors scatterplot3d Seurat SingleCellExperiment SummarizedExperiment transport VGAM]; broken = true; };
ppiStats = derive2 { name="ppiStats"; version="1.62.0"; sha256="0w5gkfah2y50x4wj5fn8i6ycx1x013mn9w4bs8r2vfqabpws1a81"; depends=[Biobase Category graph lattice RColorBrewer]; broken = true; };
predictionet = derive2 { name="predictionet"; version="1.40.0"; sha256="1f3ghlcfnls9mx2hbs923rdz7kn0wdhy2csp1y1286c5q5dybrgh"; depends=[catnet igraph MASS penalized RBGL]; broken = true; };
pulsedSilac = derive2 { name="pulsedSilac"; version="1.9.1"; sha256="1zb8xzs9h4rcrnmsfvrwb1qixn3jbnzxdwqgdrb82hgmxabmajlb"; depends=[cowplot ggplot2 ggridges MuMIn R_utils robustbase S4Vectors SummarizedExperiment UpSetR]; broken = true; };

7243
pkgs/development/r-modules/cran-packages.nix generated
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File diff suppressed because it is too large Load Diff

7
pkgs/development/r-modules/default.nix
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@ -68,9 +68,10 @@ let
hydraPlatforms = [];
};
deriveCran = mkDerive {
mkHomepage = {name, snapshot, ...}: "https://cran.r-project.org/${snapshot}/web/packages/${name}/";
mkUrls = {name, version, snapshot}: [
"https://packagemanager.rstudio.com/cran/${snapshot}/src/contrib/${name}_${version}.tar.gz"
mkHomepage = {name, ...}: "https://cran.r-project.org/web/packages/${name}/";
mkUrls = {name, version}: [
"mirror://cran/${name}_${version}.tar.gz"
"mirror://cran/Archive/${name}/${name}_${version}.tar.gz"
];
};

14
pkgs/development/r-modules/generate-r-packages.R
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@ -1,6 +1,5 @@
#!/usr/bin/env Rscript
library(data.table)
library(jsonlite)
library(parallel)
library(BiocManager)
cl <- makeCluster(10)
@ -12,13 +11,11 @@ if ("release" %in% biocVersion$BiocStatus) {
} else {
biocVersion <- max(as.numeric(as.character(biocVersion$Bioc)))
}
dates <- stream_in(url("https://packagemanager.rstudio.com/__api__/repos/2/transaction-dates"), verbose = FALSE)
snapshotDate <- as.Date(dates[nrow(dates), "alias"])
mirrorUrls <- list( bioc=paste0("http://bioconductor.statistik.tu-dortmund.de/packages/", biocVersion, "/bioc/src/contrib/")
, "bioc-annotation"=paste0("http://bioconductor.statistik.tu-dortmund.de/packages/", biocVersion, "/data/annotation/src/contrib/")
, "bioc-experiment"=paste0("http://bioconductor.statistik.tu-dortmund.de/packages/", biocVersion, "/data/experiment/src/contrib/")
, cran=paste0("https://packagemanager.rstudio.com/cran/", snapshotDate, "/src/contrib/")
, cran="https://cran.r-project.org/src/contrib/"
)
mirrorType <- commandArgs(trailingOnly=TRUE)[1]
@ -44,6 +41,10 @@ nixPrefetch <- function(name, version) {
url <- paste0(mirrorUrl, name, "_", version, ".tar.gz")
tmp <- tempfile(pattern=paste0(name, "_", version), fileext=".tar.gz")
cmd <- paste0("wget -q -O '", tmp, "' '", url, "'")
if(mirrorType == "cran"){
archiveUrl <- paste0(mirrorUrl, "Archive/", name, "/", name, "_", version, ".tar.gz")
cmd <- paste0(cmd, " || wget -q -O '", tmp, "' '", archiveUrl, "'")
}
cmd <- paste0(cmd, " && nix-hash --type sha256 --base32 --flat '", tmp, "'")
cmd <- paste0(cmd, " && echo >&2 ' added ", name, " v", version, "'")
cmd <- paste0(cmd, " ; rm -rf '", tmp, "'")
@ -74,9 +75,8 @@ formatPackage <- function(name, version, sha256, depends, imports, linkingTo) {
paste0(" ", attr, " = derive2 { name=\"", name, "\"; version=\"", version, "\"; sha256=\"", sha256, "\"; depends=[", depends, "]; };")
}
clusterExport(cl, c("nixPrefetch","readFormatted", "mirrorUrl", "knownPackages"))
clusterExport(cl, c("nixPrefetch","readFormatted", "mirrorUrl", "mirrorType", "knownPackages"))
pkgs <- as.data.table(available.packages(mirrorUrl, filters=c("R_version", "OS_type", "duplicates"), method="libcurl"))
pkgs <- pkgs[order(Package)]
write(paste("updating", mirrorType, "packages"), stderr())
@ -102,7 +102,7 @@ cat(paste("# Rscript generate-r-packages.R", mirrorType, ">new && mv new", packa
cat("\n\n")
cat("{ self, derive }:\n")
cat("let derive2 = derive ")
if (mirrorType == "cran") { cat("{ snapshot = \"", paste(snapshotDate), "\"; }", sep="")
if (mirrorType == "cran") { cat("{ }")
} else if (mirrorType == "irkernel") { cat("{}")
} else { cat("{ biocVersion = \"", biocVersion, "\"; }", sep="") }
cat(";\n")

1
pkgs/development/r-modules/generate-shell.nix
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@ -15,7 +15,6 @@ stdenv.mkDerivation {
(rWrapper.override {
packages = with rPackages; [
data_table
jsonlite
parallel
BiocManager
];