rPackages: CRAN and BioC update

2 files changed, 201 insertions, 182 deletions

diff --git a/pkgs/development/r-modules/bioc-packages.nix b/pkgs/development/r-modules/bioc-packages.nix
index 535629b8be23..4db6b91ae156 100644
--- a/pkgs/development/r-modules/bioc-packages.nix
+++ b/pkgs/development/r-modules/bioc-packages.nix
@@ -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