diff options
Diffstat (limited to 'pkgs/development/r-modules/bioc-packages.nix')
| -rw-r--r-- | pkgs/development/r-modules/bioc-packages.nix | 206 |
1 files changed, 103 insertions, 103 deletions
diff --git a/pkgs/development/r-modules/bioc-packages.nix b/pkgs/development/r-modules/bioc-packages.nix index 6d35afe1669..0c40df16015 100644 --- a/pkgs/development/r-modules/bioc-packages.nix +++ b/pkgs/development/r-modules/bioc-packages.nix @@ -20,7 +20,7 @@ in with self; { ALDEx2 = derive2 { name="ALDEx2"; version="1.32.0"; sha256="0gdkc8qwx3vpk5i09znlfrag7gk87piz61z90k96v6bm6x8sclb8"; depends=[BiocParallel GenomicRanges IRanges multtest Rfast S4Vectors SummarizedExperiment zCompositions]; }; AMARETTO = derive2 { name="AMARETTO"; version="1.16.0"; sha256="1yp2npw9mdjy0wchbp0y1r1ifyy63hdz2y3y8cia9c76nfv4627f"; 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="1.26.0"; sha256="12ml67882lscv05np4m80fg9d48dwkaa6kx5cga6x19kdx6xs2cj"; depends=[]; }; - ANCOMBC = derive2 { name="ANCOMBC"; version="2.2.1"; sha256="05gngz6cqihxg4zlf7ymw93qj61a1i19hgp4fkc0cxnkq0pambrd"; depends=[CVXR DescTools doParallel doRNG energy foreach gtools Hmisc lme4 lmerTest MASS Matrix mia multcomp nloptr Rdpack S4Vectors SingleCellExperiment SummarizedExperiment TreeSummarizedExperiment]; }; + ANCOMBC = derive2 { name="ANCOMBC"; version="2.2.2"; sha256="0jws3wqgwc0gnp7smc0lsqfw9jbcik36pl7vz9a8ndgwpp9c8653"; depends=[CVXR DescTools doParallel doRNG energy foreach gtools Hmisc lme4 lmerTest MASS Matrix mia multcomp nloptr Rdpack S4Vectors SingleCellExperiment SummarizedExperiment TreeSummarizedExperiment]; }; ANF = derive2 { name="ANF"; version="1.22.0"; sha256="08vkkfccfq8j4hanxsmjx5657kkw4qcp46qfhqvp1sd6wym69wzw"; depends=[Biobase igraph MASS RColorBrewer survival]; }; APAlyzer = derive2 { name="APAlyzer"; version="1.14.0"; sha256="1k1nrrcgx4m37z92mjvz48fx645pbsq5wi6w7h9hg0pfpynmgc26"; depends=[DESeq2 dplyr GenomicAlignments GenomicFeatures GenomicRanges ggplot2 ggrepel HybridMTest repmis Rsamtools Rsubread rtracklayer SummarizedExperiment tidyr VariantAnnotation]; }; APL = derive2 { name="APL"; version="1.4.0"; sha256="1rdc6rnb3igckg74c5297436rr4wn5bhh8mgx4scw9mry5rx5q15"; depends=[ggplot2 ggrepel magrittr org_Hs_eg_db org_Mm_eg_db plotly reticulate rlang Seurat SingleCellExperiment SummarizedExperiment topGO viridisLite]; }; @@ -44,7 +44,7 @@ in with self; { AllelicImbalance = derive2 { name="AllelicImbalance"; version="1.38.0"; sha256="1ms3x3x2gvhgllff3nwawg5jlpmgx6dhwll0dghklnv3lssbx4c7"; 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="1.14.0"; sha256="11431d453xszzjyxr10npnblhlrfw8hl5jgabpxla7cj77w02wnr"; depends=[BiocParallel data_table dplyr expm ggplot2 gtools igraph optimx plotly stringr]; }; AlpsNMR = derive2 { name="AlpsNMR"; version="4.2.0"; sha256="0rp82y7163pjbl7n6fyywh4l0sgzn1z8kp83v0kg7xk3810mj9sm"; 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="1.12.3"; sha256="0dx10gcch6csk8nw3ffz4yvn5jf0v80ynsp3dg1az0ybkqyrzbih"; depends=[BiocManager dplyr DT futile_logger htmltools httr jsonlite miniUI rapiclient rlang shiny tibble tidyr tidyselect]; }; + AnVIL = derive2 { name="AnVIL"; version="1.12.4"; sha256="05wgrr16vaqb7982j7nyri6rrhx90ljgxc37afhw190wc5dj07n0"; depends=[BiocManager dplyr DT futile_logger htmltools httr jsonlite miniUI rapiclient rlang shiny tibble tidyr tidyselect]; }; AnVILBilling = derive2 { name="AnVILBilling"; version="1.10.0"; sha256="1nxj5yn87qrzb7g8jxbqzjnllshcrfrjf0midn90xfxxj8lsfxpk"; depends=[bigrquery DBI dplyr DT ggplot2 lubridate magrittr plotly shiny shinytoastr]; }; AnVILPublish = derive2 { name="AnVILPublish"; version="1.10.0"; sha256="1b0v6dx667dpfppf69gwahxgk5sf01fzjkl3qsablqi9w7h8cnab"; depends=[AnVIL httr jsonlite readr rmarkdown whisker yaml]; }; AnVILWorkflow = derive2 { name="AnVILWorkflow"; version="1.0.1"; sha256="07s3c1c8asfswxsz9hi0sj6mrvdqa1lynsksqr8km3cssdljjf4g"; depends=[AnVIL httr jsonlite]; }; @@ -103,8 +103,8 @@ in with self; { BioCor = derive2 { name="BioCor"; version="1.24.0"; sha256="1aw8yh9l0jbjvkqgyzyr0wmwjh3ppmb0lwg8hxsfcv52ycsmvk7p"; depends=[BiocParallel GSEABase Matrix]; }; BioMM = derive2 { name="BioMM"; version="1.15.0"; sha256="01lfw0npcclcyqqh2xkhjq9jw0irbk13fsj5y1b3rz1amzzngg6p"; depends=[BiocParallel CMplot e1071 ggplot2 glmnet imager lattice nsprcomp precrec ranger rms topGO vioplot xlsx]; }; BioMVCClass = derive2 { name="BioMVCClass"; version="1.68.0"; sha256="07iay2dpq3margh1ny2snlc75g7fpfs5bf2gmhv88d31b8blg57r"; depends=[Biobase graph MVCClass Rgraphviz]; }; - BioNAR = derive2 { name="BioNAR"; version="1.2.4"; sha256="1c0sw406a95nwagb2phzdwgrhdjz44z5w6kmwb2gyi0bj8wrxbl3"; depends=[AnnotationDbi clusterCons cowplot data_table dplyr fgsea ggplot2 ggrepel GO_db igraph latex2exp minpack_lm org_Hs_eg_db poweRlaw Rdpack RSpectra rSpectral scales stringr synaptome_db viridis WGCNA]; }; - BioNERO = derive2 { name="BioNERO"; version="1.8.5"; sha256="0nrvq6cn55qzp66pqssyfxl2wh5dfqndchcv8qgfqajsnz8i35xm"; depends=[BiocParallel ComplexHeatmap dynamicTreeCut GENIE3 ggdendro ggnetwork ggplot2 ggrepel igraph intergraph matrixStats minet NetRep patchwork RColorBrewer reshape2 rlang SummarizedExperiment sva WGCNA]; }; + BioNAR = derive2 { name="BioNAR"; version="1.2.5"; sha256="0xpk3h7hpmmmcxay2w5i4by5vccxbx8rnlkxpmg2hgx0cf29vpfx"; depends=[AnnotationDbi clusterCons cowplot data_table dplyr fgsea ggplot2 ggrepel GO_db igraph latex2exp minpack_lm org_Hs_eg_db poweRlaw Rdpack RSpectra rSpectral scales stringr synaptome_db viridis WGCNA]; }; + BioNERO = derive2 { name="BioNERO"; version="1.8.7"; sha256="0yvd05yikvblnhimnmn4srcsimab4qml5k582n0c9h4rppffmvy4"; depends=[BiocParallel ComplexHeatmap dynamicTreeCut GENIE3 ggdendro ggnetwork ggplot2 ggrepel igraph intergraph matrixStats minet NetRep patchwork RColorBrewer reshape2 rlang SummarizedExperiment sva WGCNA]; }; BioNet = derive2 { name="BioNet"; version="1.60.0"; sha256="19caj3aj6gndkxkrd9s2x8v59hcdwdyxrx0ji473c3d5qrykskl1"; depends=[AnnotationDbi Biobase graph igraph RBGL]; }; BioNetStat = derive2 { name="BioNetStat"; version="1.20.0"; sha256="0bvfgppsdih6s70iizd7zh3zkb0hg4s4h1728xmyjqbvkl8fsdf4"; depends=[BiocParallel DT ggplot2 Hmisc igraph knitr markdown pathview pheatmap plyr psych RColorBrewer RJSONIO rmarkdown shiny shinyBS whisker yaml]; }; BioQC = derive2 { name="BioQC"; version="1.28.0"; sha256="0g6imi03l4xm0chx3i9wd2vdy0ls78lnylp294fq0jldl4n6y0nw"; depends=[Biobase edgeR Rcpp]; }; @@ -116,7 +116,7 @@ in with self; { BiocFHIR = derive2 { name="BiocFHIR"; version="1.2.0"; sha256="1i2yi3430gb5zhfap2yiwhwmgy34011hdk5gycb722342sl99hw4"; depends=[BiocBaseUtils dplyr DT graph jsonlite shiny tidyr visNetwork]; }; BiocFileCache = derive2 { name="BiocFileCache"; version="2.8.0"; sha256="1qk1n50arlk0mfkv9p3zl3lqbapzfkjdbadv51hsp4h9lyaw9sbg"; depends=[curl DBI dbplyr dplyr filelock httr RSQLite]; }; BiocGenerics = derive2 { name="BiocGenerics"; version="0.46.0"; sha256="19kwpis282i8x31xlh8nc3z6vvn23p3wpx7wmrqhclf8ymq61c7z"; depends=[]; }; - BiocHail = derive2 { name="BiocHail"; version="1.0.0"; sha256="0ffqhgmz5x5fy80la72fv3b93kzr52dpancddqw9hdg8ms7bxhdw"; depends=[basilisk BiocFileCache BiocGenerics dplyr reticulate]; }; + BiocHail = derive2 { name="BiocHail"; version="1.0.1"; sha256="1qn7hi7lkq3q17m7f7jb7amkph2xi7mz18yc9xgwc9hw507kr9wg"; depends=[basilisk BiocFileCache BiocGenerics dplyr reticulate]; }; BiocHubsShiny = derive2 { name="BiocHubsShiny"; version="1.0.0"; sha256="0rb73yi26wqayh5p1mf0nygpa9qyydasflc9whrvsafy8g4cfjy7"; depends=[AnnotationHub DT ExperimentHub htmlwidgets S4Vectors shiny shinyAce shinyjs shinythemes shinytoastr]; }; BiocIO = derive2 { name="BiocIO"; version="1.10.0"; sha256="03hslg7k6khchf54gmlbkvwbkfn5ppz0wp7lh75gsnr0licsjkwx"; depends=[BiocGenerics S4Vectors]; }; BiocNeighbors = derive2 { name="BiocNeighbors"; version="1.18.0"; sha256="1i4b37n9darizfq9i4vvbnxgrwhkvvd25a4cpfjv7nqywjfbsfjd"; depends=[BiocParallel Matrix Rcpp RcppHNSW S4Vectors]; }; @@ -126,12 +126,12 @@ in with self; { BiocSet = derive2 { name="BiocSet"; version="1.14.0"; sha256="1q5794gsinpy9hv5n1vx79bkqxi1jxzxjl95jlw9pqjmlnki07i5"; depends=[AnnotationDbi BiocIO dplyr KEGGREST ontologyIndex plyr rlang S4Vectors tibble tidyr]; }; BiocSingular = derive2 { name="BiocSingular"; version="1.16.0"; sha256="1a33zsw353pryq30178sbj9jzsmb4m7spqbx11hsicri8s1c0lb9"; depends=[beachmat BiocGenerics BiocParallel DelayedArray irlba Matrix Rcpp rsvd S4Vectors ScaledMatrix]; }; BiocSklearn = derive2 { name="BiocSklearn"; version="1.22.0"; sha256="0ggzln6ld4a4a3n2swssm11saj0pnqgsfibd0w1aa4k0q2i5m3dy"; depends=[basilisk reticulate SummarizedExperiment]; }; - BiocStyle = derive2 { name="BiocStyle"; version="2.28.0"; sha256="04npnfmz1p1vpwrdsim309k7518i4p1li04xnmw8c9zgdb6yl61a"; depends=[BiocManager bookdown knitr rmarkdown yaml]; }; + BiocStyle = derive2 { name="BiocStyle"; version="2.28.1"; sha256="11v3gzy88fai0rhdymvj9k74g7hjc6n9fihfrrnw0qfr447z1d61"; depends=[BiocManager bookdown knitr rmarkdown yaml]; }; BiocVersion = derive2 { name="BiocVersion"; version="3.17.1"; sha256="0n29adnb62agp9li8rmn68z653d2m41iy9zjz75h43a05drlgp33"; depends=[]; }; BiocWorkflowTools = derive2 { name="BiocWorkflowTools"; version="1.26.0"; sha256="1zvjj0hpqwdv7yifqwyb14166ppxw91d964gz4xclism5z5lvyln"; depends=[BiocStyle bookdown git2r httr knitr rmarkdown rstudioapi stringr usethis]; }; Biostrings = derive2 { name="Biostrings"; version="2.68.1"; sha256="13cnjbq2iykv83ycb4151d7yys21s3v15fc72v3s02m1i92lqyq4"; depends=[BiocGenerics crayon GenomeInfoDb IRanges S4Vectors XVector]; }; BloodGen3Module = derive2 { name="BloodGen3Module"; version="1.8.0"; sha256="167wpz0s9xlgpp1d3rfy7p76wgmsqlxcj9g7dbz3y0qv7iilngck"; depends=[circlize ComplexHeatmap ExperimentHub ggplot2 gtools limma matrixStats preprocessCore randomcoloR reshape2 SummarizedExperiment testthat V8]; }; - BridgeDbR = derive2 { name="BridgeDbR"; version="2.10.0"; sha256="0372bafv2nxs61wr3dinn6px7qvbswysnacv2xdrp3gm5i1wjzsi"; depends=[curl rJava]; }; + BridgeDbR = derive2 { name="BridgeDbR"; version="2.10.2"; sha256="11rjv5dlkyjsq43b9yi80mf8imxigqmlrzhk7v65j9lq7kdlcd7d"; depends=[curl rJava]; }; BrowserViz = derive2 { name="BrowserViz"; version="2.22.0"; sha256="14ddcfl73bi4ivd6wqp9xfxaf7fx89gh6qzf91psj44vyvzmdar3"; depends=[BiocGenerics httpuv jsonlite]; }; BubbleTree = derive2 { name="BubbleTree"; version="2.30.0"; sha256="17c97x8g34fqsq3cnj4cp4cjignn7d8m31k1msinxy92kndij3sw"; depends=[Biobase BiocGenerics BiocStyle biovizBase dplyr e1071 GenomicRanges ggplot2 gridExtra gtable gtools IRanges limma magrittr plyr RColorBrewer WriteXLS]; }; BufferedMatrix = derive2 { name="BufferedMatrix"; version="1.64.0"; sha256="0sjz4ymqdn57l6cr0968w5nbhp5fm386cf2waxph8n7s1w4lraf3"; depends=[]; }; @@ -181,7 +181,7 @@ in with self; { CONSTANd = derive2 { name="CONSTANd"; version="1.8.0"; sha256="083pqvzxd3svy8g9qrv08221dr2rcwj9jknask2h227zi4id1lwi"; depends=[]; }; CORREP = derive2 { name="CORREP"; version="1.66.0"; sha256="1gsjkn72npj78xs2j00ny5vcykfx9j6j41nckk2lnmsq2vynjj95"; depends=[e1071]; }; COSNet = derive2 { name="COSNet"; version="1.34.0"; sha256="1qjayfvb4iy8jpyq547gs2x66p99j56v6zd443rjn0rrwqyrxw9m"; depends=[]; }; - COTAN = derive2 { name="COTAN"; version="2.0.4"; sha256="0f2x7xra32m4pnpr95wprmi4na8vqc0rps5jyhaq4d1p2r9zrlil"; depends=[assertthat circlize ComplexHeatmap dendextend dplyr factoextra ggplot2 ggrepel ggthemes irlba Matrix parallelly plyr RColorBrewer Rfast rlang scales Seurat stringr tibble tidyr umap withr zeallot]; }; + COTAN = derive2 { name="COTAN"; version="2.0.5"; sha256="1blrziycc3xgglk1r2hqvz4qiqjvnyjzvjlvcjwvm3yij11wwl5q"; depends=[assertthat circlize ComplexHeatmap dendextend dplyr factoextra ggplot2 ggrepel ggthemes irlba Matrix parallelly plyr RColorBrewer Rfast rlang scales Seurat stringr tibble tidyr umap withr zeallot]; }; CRISPRseek = derive2 { name="CRISPRseek"; version="1.40.0"; sha256="0gp96c3gip48yd2ffw6n9p30ib7yiz7p4h57i0kc4qv3lnj31dqi"; depends=[BiocGenerics Biostrings BSgenome data_table DelayedArray dplyr GenomeInfoDb GenomicRanges hash IRanges keras mltools reticulate rhdf5 S4Vectors seqinr XVector]; }; CRImage = derive2 { name="CRImage"; version="1.48.0"; sha256="11ikg8mil9slnjxcl45b97i2yng8bh1fdcyf92bwhrwnamp0asfc"; depends=[aCGH DNAcopy e1071 EBImage foreach MASS sgeostat]; }; CSAR = derive2 { name="CSAR"; version="1.52.0"; sha256="0p3r2x7gn4gmsdmymwi1spd4dpc8phgbg7zw8hwbif0s28vpz40m"; depends=[GenomeInfoDb GenomicRanges IRanges S4Vectors]; }; @@ -209,7 +209,7 @@ in with self; { ChAMP = derive2 { name="ChAMP"; version="2.30.0"; sha256="1px2pm90lxwh0yn7h1kmmf94flhjs5p4i0iav7ya1xfybyg4w2zc"; depends=[bumphunter ChAMPdata combinat dendextend DMRcate DNAcopy doParallel DT GenomicRanges ggplot2 globaltest goseq Hmisc Illumina450ProbeVariants_db IlluminaHumanMethylation450kmanifest IlluminaHumanMethylationEPICanno_ilm10b4_hg19 IlluminaHumanMethylationEPICmanifest illuminaio impute isva kpmt limma marray matrixStats minfi missMethyl plotly plyr preprocessCore prettydoc quadprog qvalue RColorBrewer rmarkdown RPMM shiny shinythemes sva wateRmelon]; }; ChIC = derive2 { name="ChIC"; version="1.19.0"; sha256="0zbmhixxn3skn8csz93fyyfamz1n3gzjzb2caw8ybi2cysgzz5ys"; depends=[BiocGenerics caret caTools ChIC_data genomeIntervals GenomicRanges IRanges progress randomForest Rsamtools S4Vectors]; }; ChIPComp = derive2 { name="ChIPComp"; version="1.30.0"; sha256="1v27bqik5cgcvs1kb67s52r56v6fakvmi81iybvvvbxvcn1dmy9r"; depends=[BiocGenerics BSgenome_Hsapiens_UCSC_hg19 BSgenome_Mmusculus_UCSC_mm9 GenomeInfoDb GenomicRanges IRanges limma Rsamtools rtracklayer S4Vectors]; }; - ChIPQC = derive2 { name="ChIPQC"; version="1.36.0"; sha256="0fpgjiixkb885dbhh70r0g6mib1yz2cyfw3v5wcjxhbzfrn27wqh"; depends=[Biobase BiocGenerics BiocParallel chipseq DiffBind GenomicAlignments GenomicFeatures GenomicRanges ggplot2 gtools IRanges Nozzle_R1 reshape2 Rsamtools S4Vectors TxDb_Celegans_UCSC_ce6_ensGene TxDb_Dmelanogaster_UCSC_dm3_ensGene TxDb_Hsapiens_UCSC_hg18_knownGene TxDb_Hsapiens_UCSC_hg19_knownGene TxDb_Mmusculus_UCSC_mm10_knownGene TxDb_Mmusculus_UCSC_mm9_knownGene TxDb_Rnorvegicus_UCSC_rn4_ensGene]; }; + ChIPQC = derive2 { name="ChIPQC"; version="1.36.1"; sha256="0jlh74gr4d9n7g91mcgg82yha9hvd5kqkqn8r36knbxs27drbxbc"; depends=[Biobase BiocGenerics BiocParallel chipseq DiffBind GenomicAlignments GenomicFeatures GenomicRanges ggplot2 gtools IRanges Nozzle_R1 reshape2 Rsamtools S4Vectors TxDb_Celegans_UCSC_ce6_ensGene TxDb_Dmelanogaster_UCSC_dm3_ensGene TxDb_Hsapiens_UCSC_hg18_knownGene TxDb_Hsapiens_UCSC_hg19_knownGene TxDb_Mmusculus_UCSC_mm10_knownGene TxDb_Mmusculus_UCSC_mm9_knownGene TxDb_Rnorvegicus_UCSC_rn4_ensGene]; }; ChIPXpress = derive2 { name="ChIPXpress"; version="1.44.0"; sha256="08qzmjvz3v5ji9lzpxlhxgv3d0smmyvai49yphbbvz9vv57hgjkf"; depends=[affy biganalytics bigmemory Biobase ChIPXpressData frma GEOquery]; }; ChIPanalyser = derive2 { name="ChIPanalyser"; version="1.22.0"; sha256="1r8d5bvmmgcxw8kxzdgymwnyg0lspjv9sfjd6pfrhjn88sjz22xv"; depends=[BiocManager Biostrings BSgenome GenomeInfoDb GenomicRanges IRanges RColorBrewer RcppRoll ROCR rtracklayer S4Vectors]; }; ChIPexoQual = derive2 { name="ChIPexoQual"; version="1.24.0"; sha256="1iysqs2k0xxiwd48ymahf6rywwj9ingjcfmnhx9d1x6w2h00v7lz"; depends=[BiocParallel biovizBase broom data_table dplyr GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 hexbin IRanges RColorBrewer rmarkdown Rsamtools S4Vectors scales viridis]; }; @@ -224,7 +224,7 @@ in with self; { ChromSCape = derive2 { name="ChromSCape"; version="1.10.0"; sha256="1v5gym0zsbi0jwpgdr442z97zw295f0h335jndzbi23n4nfj6lxv"; depends=[batchelor BiocParallel colorRamps colourpicker ConsensusClusterPlus coop DelayedArray dplyr DT edgeR forcats fs GenomicRanges gggenes ggplot2 ggrepel gridExtra IRanges irlba jsonlite kableExtra Matrix matrixTests msigdbr plotly qs qualV Rcpp rlist Rsamtools rtracklayer Rtsne S4Vectors scater scran shiny shinycssloaders shinydashboard shinydashboardPlus shinyFiles shinyhelper shinyjs shinyWidgets SingleCellExperiment stringdist stringr SummarizedExperiment tibble tidyr umap viridis]; }; CircSeqAlignTk = derive2 { name="CircSeqAlignTk"; version="1.2.0"; sha256="199ynhjl4hmgxwgzpg2wp4k5jrw737c7v40yjg7ds17j62hs4ari"; depends=[BiocGenerics Biostrings dplyr ggplot2 IRanges magrittr Rbowtie2 Rhisat2 rlang Rsamtools S4Vectors ShortRead tidyr]; }; CiteFuse = derive2 { name="CiteFuse"; version="1.12.0"; sha256="1cvg7gnnjxgickqd3hm90dv5zi1vr3xv0l51qll7gfksck75d8fr"; depends=[compositions cowplot dbscan ggplot2 ggraph ggridges gridExtra igraph Matrix mixtools pheatmap randomForest Rcpp reshape2 rhdf5 rlang Rtsne S4Vectors scales scran SingleCellExperiment SummarizedExperiment uwot]; }; - ClassifyR = derive2 { name="ClassifyR"; version="3.4.9"; sha256="00l0xdp4llyf96k8lnzb3s4ani785myvrlqd5zmvazp0vcdaryn1"; depends=[BiocParallel dplyr genefilter generics ggplot2 ggpubr MultiAssayExperiment ranger reshape2 rlang S4Vectors survival tidyr]; }; + ClassifyR = derive2 { name="ClassifyR"; version="3.4.11"; sha256="10mcc62v4fzm8gavs874dmkhnqz8vdl52di3z2qjg76jv6jj7z9q"; depends=[BiocParallel dplyr genefilter generics ggplot2 ggpubr MultiAssayExperiment ranger reshape2 rlang S4Vectors survival tidyr]; }; Clomial = derive2 { name="Clomial"; version="1.36.0"; sha256="1y4jjq9vxgi6m5g94j0j4xvcbpba7pv6y284ig3m4m83pq9xbq5d"; depends=[matrixStats permute]; }; Clonality = derive2 { name="Clonality"; version="1.47.0"; sha256="0yxwwc0sl3impvzr0bmjmdn65z6qx6lf5pwik2p8wxxgaybvff9r"; depends=[DNAcopy]; }; CluMSID = derive2 { name="CluMSID"; version="1.16.0"; sha256="1p210mc7akhsxbq8daqk9lqxnmlykmjgrsyliiq3n7qm6z4md2pl"; depends=[ape Biobase dbscan GGally ggplot2 gplots MSnbase mzR network plotly RColorBrewer S4Vectors sna]; }; @@ -250,7 +250,7 @@ in with self; { CytoML = derive2 { name="CytoML"; version="2.12.0"; sha256="19rlg15nk2205vma4whpqmvlazww5i3ibxhmk9cljsaj4ql560vf"; depends=[BH Biobase cpp11 cytolib data_table dplyr flowCore flowWorkspace ggcyto graph jsonlite openCyto RBGL Rgraphviz Rhdf5lib RProtoBufLib tibble XML yaml]; }; CytoPipeline = derive2 { name="CytoPipeline"; version="1.0.2"; sha256="0xp1fqs87q9k52g3c2181nn7jfrzmahhafzsaw4saaynsdh7hnhl"; depends=[BiocFileCache BiocParallel diagram flowAI flowCore ggcyto ggplot2 jsonlite PeacoQC rlang scales withr]; }; DAMEfinder = derive2 { name="DAMEfinder"; version="1.12.0"; sha256="0m8g1sp55mxa0qswpqkzk73myhhy3s49c21hf97sk0lxis5lagcd"; depends=[BiocGenerics Biostrings bumphunter cowplot GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 IRanges limma plyr readr reshape2 Rsamtools S4Vectors stringr SummarizedExperiment VariantAnnotation]; }; - DAPAR = derive2 { name="DAPAR"; version="1.32.2"; sha256="1gbcwjwmqdimics2c7dnlwsf5l2fs48mcrjhhyjh0xnsmvgsp16m"; depends=[Biobase DAPARdata foreach highcharter MSnbase]; }; + DAPAR = derive2 { name="DAPAR"; version="1.32.5"; sha256="0jjllbp9szlvbrfc74lvw8i9q7zibxinvvnmf3xgv654xkv218pv"; depends=[Biobase DAPARdata foreach highcharter MSnbase]; }; DART = derive2 { name="DART"; version="1.48.0"; sha256="0rkabvjkh5iimpxspyizpffz69q7pvj1jq3f9704a2p51q60j74n"; depends=[igraph]; }; DECIPHER = derive2 { name="DECIPHER"; version="2.28.0"; sha256="16z6yk8rr2115z6g1l7fl01binxm29vnxsnsm2wzfvc5vv49927n"; depends=[Biostrings DBI IRanges RSQLite S4Vectors XVector]; }; DEFormats = derive2 { name="DEFormats"; version="1.28.0"; sha256="1dqiy0q1w3n9r03bxhx2vnk1z5a476rpkzcwl3cn9ghqns2wvmlz"; depends=[checkmate data_table DESeq2 edgeR GenomicRanges S4Vectors SummarizedExperiment]; }; @@ -267,7 +267,7 @@ in with self; { DEqMS = derive2 { name="DEqMS"; version="1.18.0"; sha256="0hgra7dvrfqniwz8srnqsx6mhd6pjx4bn9dfy0fyp4sldj8d1d83"; depends=[ggplot2 limma matrixStats]; }; DEsingle = derive2 { name="DEsingle"; version="1.20.0"; sha256="145kpcp3v4wg7fjq4m1a15ikvwdpqc753217rjpr5p5306j489ra"; depends=[bbmle BiocParallel gamlss MASS Matrix maxLik pscl VGAM]; }; DEsubs = derive2 { name="DEsubs"; version="1.26.0"; sha256="1mzq5lld6hh1pg6j3z88h3rydr984qb5kh92bzxqqlj8j1lhlmif"; depends=[circlize DESeq2 EBSeq edgeR ggplot2 graph igraph jsonlite limma locfit Matrix NBPSeq pheatmap RBGL]; }; - DExMA = derive2 { name="DExMA"; version="1.8.0"; sha256="0k6il16z49jczk6kgcp849n44jymid2ck17s3cx2x79dgp6c6x5p"; depends=[Biobase bnstruct DExMAdata GEOquery impute limma pheatmap plyr RColorBrewer scales snpStats sva swamp]; }; + DExMA = derive2 { name="DExMA"; version="1.8.1"; sha256="1c5ha2afscqh8yr1hpsl98x291g8awg0jnkb97yv2cmwwg8dbipg"; depends=[Biobase bnstruct DExMAdata GEOquery impute limma pheatmap plyr RColorBrewer scales snpStats sva swamp]; }; DFP = derive2 { name="DFP"; version="1.58.0"; sha256="1z4d7q5aqb3a5ma438v2y7ikjnlrfncm02adaj5krxlyqcsjksci"; depends=[Biobase]; }; DIAlignR = derive2 { name="DIAlignR"; version="2.8.0"; sha256="1fms2yrwhgv1qhdq30zzbgqli9ir99iqmi41hgr624x6jrbpy8fy"; 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="1.14.0"; sha256="1frp3czy4zry1ml2r93aw2h8arr5bfxlszimcnmqpbca0gxd6lx3"; depends=[arm benchmarkme BiocParallel data_table fastDummies GenomicRanges IRanges MASS matrixStats rtracklayer S4Vectors speedglm SummarizedExperiment tibble]; }; @@ -281,7 +281,7 @@ in with self; { DNAcopy = derive2 { name="DNAcopy"; version="1.74.1"; sha256="1bj87ksvch5cm5zxwgfiiql0j94pvzbpn59wp6bacyip65z7w3ax"; depends=[]; }; DNAfusion = derive2 { name="DNAfusion"; version="1.2.0"; sha256="1wakfplnc513r31pqbpdvmdc0qqbrh5naizb764jj3nqvs1h3wfj"; depends=[bamsignals BiocBaseUtils BiocGenerics GenomicAlignments GenomicFeatures GenomicRanges IRanges Rsamtools S4Vectors TxDb_Hsapiens_UCSC_hg38_knownGene]; }; DNAshapeR = derive2 { name="DNAshapeR"; version="1.28.0"; sha256="03sfa8cyfrvww1nihv1dg7d5c5qkf6j2w9d0v5zfww2dp93i504k"; depends=[Biostrings fields GenomicRanges Rcpp]; }; - DOSE = derive2 { name="DOSE"; version="3.26.1"; sha256="1whvgzw8p0nm3kchdndrxj4x3fhmq0vgbz77d54sqq1qri4j35qx"; depends=[AnnotationDbi BiocParallel fgsea ggplot2 GOSemSim HDO_db qvalue reshape2]; }; + DOSE = derive2 { name="DOSE"; version="3.26.2"; sha256="07hhvyv1yiblpx8yvnx919jhafl89s56lfkjiyihv4yzqn16ln3d"; depends=[AnnotationDbi BiocParallel fgsea ggplot2 GOSemSim HDO_db qvalue reshape2]; }; DRIMSeq = derive2 { name="DRIMSeq"; version="1.28.0"; sha256="1i9lcp31g94mllkwcyfablj27qr8v7vqk9j96ywrdfpj8dmcrw98"; depends=[BiocGenerics BiocParallel edgeR GenomicRanges ggplot2 IRanges limma MASS reshape2 S4Vectors]; }; DSS = derive2 { name="DSS"; version="2.48.0"; sha256="1aslbzwqfp609ym98k6cjjf6r1ns9hxcpx4igfjhqf2v0pazz2q8"; depends=[Biobase BiocParallel bsseq]; }; DTA = derive2 { name="DTA"; version="2.46.0"; sha256="1hi0i76sr0naq06py8bx3cm5wb4v3haz9wa2rnznpzw67svhxci9"; depends=[LSD scatterplot3d]; }; @@ -294,12 +294,12 @@ in with self; { DegNorm = derive2 { name="DegNorm"; version="1.10.1"; sha256="01jg6wgz0117kvjjmsnv8whizyd3iayfsvhgd615hjzz0fm82szp"; depends=[data_table doParallel foreach GenomicAlignments GenomicFeatures GenomicRanges ggplot2 heatmaply IRanges plotly plyr Rcpp RcppArmadillo Rsamtools S4Vectors viridis]; }; DelayedArray = derive2 { name="DelayedArray"; version="0.26.7"; sha256="1xsq85nm1gk537mw6ppsyykpw70kczv6wn1nll63b0k8xs4wj0ha"; depends=[BiocGenerics IRanges Matrix MatrixGenerics S4Arrays S4Vectors]; }; DelayedDataFrame = derive2 { name="DelayedDataFrame"; version="1.16.0"; sha256="00668ijn1jd6j503z0ayy0i7i81qazga0bvsa2qlfbbyqyasbmhk"; depends=[BiocGenerics DelayedArray S4Vectors]; }; - DelayedMatrixStats = derive2 { name="DelayedMatrixStats"; version="1.22.1"; sha256="13iqlw74zh65y2ckwg0b3xbqc6jgj34xjgsg9axfv7j7znwk9igg"; depends=[DelayedArray IRanges Matrix MatrixGenerics matrixStats S4Vectors sparseMatrixStats]; }; + DelayedMatrixStats = derive2 { name="DelayedMatrixStats"; version="1.22.6"; sha256="0jaaqa2fm61dmsphm5y4rlwf2dm1l5rs0vpq0f5r35iyw2m12lh8"; depends=[DelayedArray IRanges Matrix MatrixGenerics matrixStats S4Vectors sparseMatrixStats]; }; DelayedRandomArray = derive2 { name="DelayedRandomArray"; version="1.8.0"; sha256="0dly19l7739icsww053ds6lqg26x2z6lmyaf1hsqgpy3lczfr2hv"; depends=[BH DelayedArray dqrng Rcpp]; }; DelayedTensor = derive2 { name="DelayedTensor"; version="1.6.0"; sha256="18qk3wi15ixjdfkfviy8qaqqs4cvr8dk25bjnr8sq4gnx73iy34p"; depends=[BiocSingular DelayedArray DelayedRandomArray einsum HDF5Array irlba Matrix rTensor]; }; DepInfeR = derive2 { name="DepInfeR"; version="1.4.0"; sha256="1xw8y5bnki8p8khp4161kfrl5jicv4acf6vds0lfvzblgkh676jr"; depends=[BiocParallel glmnet matrixStats]; }; DepecheR = derive2 { name="DepecheR"; version="1.16.0"; sha256="1kn1w1fs19gjvg8nhbvj6hyp32h6k81dnal4ab12xl1jgaa3xj5p"; depends=[beanplot doSNOW dplyr FNN foreach ggplot2 gmodels gplots MASS matrixStats mixOmics moments Rcpp RcppEigen reshape2 robustbase viridis]; }; - DiffBind = derive2 { name="DiffBind"; version="3.10.0"; sha256="1p5fxfpvjz85a2n1jsmj3niqzymnlsja9b53q2yxvj327qq58z8a"; depends=[amap apeglm ashr BiocParallel DESeq2 dplyr GenomicAlignments GenomicRanges ggplot2 ggrepel gplots GreyListChIP IRanges lattice limma locfit RColorBrewer Rcpp Rhtslib Rsamtools S4Vectors SummarizedExperiment systemPipeR]; }; + DiffBind = derive2 { name="DiffBind"; version="3.10.1"; sha256="12frl2wfvfz4gpq4fjsmglqyqfxdk3zjbhqkc78rzylbw37xx3bf"; depends=[amap apeglm ashr BiocParallel DESeq2 dplyr GenomicAlignments GenomicRanges ggplot2 ggrepel gplots GreyListChIP IRanges lattice limma locfit RColorBrewer Rcpp Rhtslib Rsamtools S4Vectors SummarizedExperiment systemPipeR]; }; DiffLogo = derive2 { name="DiffLogo"; version="2.24.0"; sha256="0wj9k3nnm5y1j5989i2gngxnhsygm9z5mbm532m174hap0fddpy9"; depends=[cba]; }; DifferentialRegulation = derive2 { name="DifferentialRegulation"; version="1.4.2"; sha256="0dgi4jpianzsqrmkc0mj6cbn4y196mr9fk9h3m10xvgmyvw9gbly"; depends=[BANDITS data_table doParallel doRNG foreach ggplot2 MASS Matrix Rcpp RcppArmadillo SingleCellExperiment SummarizedExperiment tximport]; }; Dino = derive2 { name="Dino"; version="1.6.0"; sha256="12zsj95nd9xvn62bfw45a42bqdqkxhzs4p8r4pww7dslh75hjpzv"; depends=[BiocParallel BiocSingular Matrix matrixStats S4Vectors scran Seurat SingleCellExperiment SummarizedExperiment]; }; @@ -325,7 +325,7 @@ in with self; { EGSEA = derive2 { name="EGSEA"; version="1.28.0"; sha256="008id8nmf5aa2vzh9is7v0fvgljgndz2b37dnnc4w4d16399bm0z"; depends=[AnnotationDbi Biobase DT edgeR EGSEAdata gage ggplot2 globaltest gplots GSVA HTMLUtils htmlwidgets hwriter limma metap org_Hs_eg_db org_Mm_eg_db org_Rn_eg_db PADOG pathview plotly RColorBrewer safe stringi topGO]; }; ELMER = derive2 { name="ELMER"; version="2.24.1"; sha256="1dk0glasd5rrilbbdf7nql7yn8n8gp7cvhbbl51949v71qndxpn9"; depends=[biomaRt circlize ComplexHeatmap DelayedArray doParallel downloader dplyr ELMER_data GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 ggpubr ggrepel gridExtra Gviz IRanges lattice magrittr Matrix MultiAssayExperiment plotly plyr progress purrr readr reshape reshape2 rmarkdown rtracklayer rvest S4Vectors scales stringr SummarizedExperiment TCGAbiolinks tibble tidyr xml2]; }; EMDomics = derive2 { name="EMDomics"; version="2.30.0"; sha256="1kmv75qj51jjrbqm8ydwrskp1r11z3jmhiyb2vl7sh40dqv69hn3"; depends=[BiocParallel CDFt emdist ggplot2 matrixStats preprocessCore]; }; - ENmix = derive2 { name="ENmix"; version="1.36.03"; sha256="1kj4w0ky99lz5k236zj2s062lrm7dl5mp606ar8vhag8r6a987gx"; depends=[AnnotationHub Biobase doParallel dynamicTreeCut ExperimentHub foreach genefilter geneplotter gplots gtools illuminaio impute IRanges matrixStats minfi quadprog RPMM S4Vectors SummarizedExperiment]; }; + ENmix = derive2 { name="ENmix"; version="1.36.08"; sha256="1pvyz9a2cmdmci7fisk2rhbq2fjvpc953w9rsf6k9drkgs466506"; depends=[AnnotationHub Biobase doParallel dynamicTreeCut ExperimentHub foreach genefilter geneplotter gplots gtools illuminaio impute IRanges irlba matrixStats minfi quadprog RPMM S4Vectors SummarizedExperiment]; }; ERSSA = derive2 { name="ERSSA"; version="1.18.0"; sha256="1gzd2g837g4iqmjc2vd9f0bg5va0prnam7nd1hvr0rdkg3l525fw"; depends=[BiocParallel DESeq2 edgeR ggplot2 plyr RColorBrewer]; }; EWCE = derive2 { name="EWCE"; version="1.8.2"; sha256="0di7qbw3yrry44fxcfnksxpf41pdl91xjrxc6cpajlmlyzgarp66"; depends=[BiocParallel data_table DelayedArray dplyr ewceData ggplot2 HGNChelper limma Matrix orthogene reshape2 RNOmni SingleCellExperiment stringr SummarizedExperiment]; }; EasyCellType = derive2 { name="EasyCellType"; version="1.2.0"; sha256="1l68g7hlcfmszf9sg1nagkv00sgd80klgi25jizabj6c1mg0pm13"; depends=[AnnotationDbi clusterProfiler dplyr forcats ggplot2 magrittr org_Hs_eg_db org_Mm_eg_db rlang]; }; @@ -342,7 +342,7 @@ in with self; { ExCluster = derive2 { name="ExCluster"; version="1.18.0"; sha256="0ji516fx1mai38jb685gj538wsyg2ivplsf731nlhqwpg4zzc0cs"; depends=[GenomicRanges IRanges matrixStats Rsubread rtracklayer]; }; ExiMiR = derive2 { name="ExiMiR"; version="2.42.0"; sha256="17vdlgriwm6imkfnksgcjrg0gj8zygwnhlahxlrc1qnllcv78f6c"; depends=[affy affyio Biobase limma preprocessCore]; }; ExperimentHub = derive2 { name="ExperimentHub"; version="2.8.1"; sha256="1md6lan98h95jv776zyvl5im39gz4h6fdxw571vfahgr4b2nxvm4"; depends=[AnnotationHub BiocFileCache BiocGenerics BiocManager rappdirs S4Vectors]; }; - ExperimentHubData = derive2 { name="ExperimentHubData"; version="1.26.0"; sha256="13il34lhb0qzl40995g9pf15r7m0l9hm4di32pig8jlg93qcnqgs"; depends=[AnnotationHubData BiocGenerics BiocManager curl DBI ExperimentHub httr S4Vectors]; }; + ExperimentHubData = derive2 { name="ExperimentHubData"; version="1.26.1"; sha256="0r6p6h5hvz8wqxwnw1ad0ibfvx8qkvx6nbykm9b9dbbk14kl6rn7"; depends=[AnnotationHubData BiocGenerics BiocManager curl DBI ExperimentHub httr S4Vectors]; }; ExperimentSubset = derive2 { name="ExperimentSubset"; version="1.10.0"; sha256="135c67l02m5nj7g72rwwwhdg4jdlqjxjj62rs4nvp1qla779amh7"; depends=[Matrix S4Vectors SingleCellExperiment SpatialExperiment SummarizedExperiment TreeSummarizedExperiment]; }; ExploreModelMatrix = derive2 { name="ExploreModelMatrix"; version="1.12.0"; sha256="01lkshvlc7f9fd8gyzk9kymq6k3a4h00vpg1blm9b723rbj9jb2d"; depends=[cowplot dplyr DT ggplot2 limma magrittr MASS rintrojs S4Vectors scales shiny shinydashboard shinyjs tibble tidyr]; }; ExpressionAtlas = derive2 { name="ExpressionAtlas"; version="1.28.0"; sha256="1vr2lc06qqp33nx15kiw9pq1h6rqf09ngwgkmafxqk8lsiw5i44j"; depends=[Biobase BiocStyle httr jsonlite limma RCurl S4Vectors SummarizedExperiment XML xml2]; }; @@ -371,12 +371,12 @@ in with self; { GAprediction = derive2 { name="GAprediction"; version="1.26.0"; sha256="1sr3dj6w6mcvypakcryw0zkdjkp1lzx4wjc9jrwq04cqclq8dyqd"; depends=[glmnet Matrix]; }; GBScleanR = derive2 { name="GBScleanR"; version="1.4.4"; sha256="1z3acpy4cxw9q92bzfd5c8b4mnj6zg2akg575ygr5fzbxb0fk7rc"; depends=[expm gdsfmt ggplot2 Rcpp RcppParallel SeqArray tidyr]; }; GCSscore = derive2 { name="GCSscore"; version="1.14.0"; sha256="0fqr0sgplpbkdpvwgi8fpmwmnqja41622pvkkzsalbzai021hgp3"; depends=[affxparser Biobase BiocManager data_table devtools dplR RSQLite stringr]; }; - GDCRNATools = derive2 { name="GDCRNATools"; version="1.20.0"; sha256="1fspvlj7x80prsvj0q53y5m05b584ajrivrxpr8ijnnqam4fy6nb"; depends=[BiocParallel biomaRt clusterProfiler DESeq2 DOSE DT edgeR GenomicDataCommons ggplot2 gplots jsonlite limma org_Hs_eg_db pathview rjson shiny survival survminer XML]; }; + GDCRNATools = derive2 { name="GDCRNATools"; version="1.20.1"; sha256="1s80vqh5z7zvf0vjfhwvd6rxc9s96fvqv528px9dlxv6fl52g103"; depends=[BiocParallel biomaRt clusterProfiler DESeq2 DOSE DT edgeR GenomicDataCommons ggplot2 gplots jsonlite limma org_Hs_eg_db pathview rjson shiny survival survminer XML]; }; GDSArray = derive2 { name="GDSArray"; version="1.20.0"; sha256="0p2mw6j04cr08yw1rnjsddb4fm24h973m7pr8rznzsjnki3r944w"; depends=[BiocGenerics DelayedArray gdsfmt S4Vectors SeqArray SNPRelate]; }; GEM = derive2 { name="GEM"; version="1.26.0"; sha256="1dr3d2jsbzk858wnbqgv2gy2qspx9sg49lmqvb8wl4m01jm3zbb4"; depends=[ggplot2]; }; GENESIS = derive2 { name="GENESIS"; version="2.30.0"; sha256="0lbd8fqv3j1wkc17ah30ylfskj29cvb8d61xlja430kfkfky2n97"; depends=[Biobase BiocGenerics BiocParallel data_table gdsfmt GenomicRanges GWASTools igraph IRanges Matrix reshape2 S4Vectors SeqArray SeqVarTools SNPRelate]; }; GENIE3 = derive2 { name="GENIE3"; version="1.22.0"; sha256="1q4wi3k95c8vsyfx6359p2p29ascjg1cxmpp9bf99ixbjs71rd33"; depends=[dplyr reshape2]; }; - GEOexplorer = derive2 { name="GEOexplorer"; version="1.6.0"; sha256="1dh94sh3zypqkvgijmhi6jcsqnh5hha178vcmsk7xfbdrrqjcdva"; depends=[Biobase DT factoextra GEOquery ggplot2 heatmaply htmltools impute limma maptools pheatmap plotly scales shiny shinyBS shinybusy shinyHeatmaply stringr umap]; }; + GEOexplorer = derive2 { name="GEOexplorer"; version="1.6.0"; sha256="1dh94sh3zypqkvgijmhi6jcsqnh5hha178vcmsk7xfbdrrqjcdva"; depends=[Biobase DT factoextra GEOquery ggplot2 heatmaply htmltools impute limma pheatmap plotly scales shiny shinyBS shinybusy shinyHeatmaply stringr umap]; }; GEOfastq = derive2 { name="GEOfastq"; version="1.8.0"; sha256="0nb8a83i0v7pjrximzqjfrcflxdhbv7y2gjz9bcy20yvcgzi6pn8"; depends=[doParallel foreach plyr RCurl rvest stringr xml2]; }; GEOmetadb = derive2 { name="GEOmetadb"; version="1.62.0"; sha256="0xlm1yf2n2wi8sy6b4l7bnkb5dzgd2nfnpp2wrxncp163rrxi40q"; depends=[GEOquery RSQLite]; }; GEOquery = derive2 { name="GEOquery"; version="2.68.0"; sha256="1xyrfj8b7j2wdjlbmwhx1c0hfbvr7l7jxyw2v64fbw8604zprv4s"; depends=[Biobase curl data_table dplyr limma magrittr R_utils readr tidyr xml2]; }; @@ -420,6 +420,7 @@ in with self; { GenVisR = derive2 { name="GenVisR"; version="1.31.1"; sha256="0507hmgv3gl8rl7hnha387yjsmhv9hfysvm4s9whqpqsgm5d4iqp"; depends=[AnnotationDbi BiocGenerics biomaRt Biostrings BSgenome data_table DBI GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 gridExtra gtable gtools IRanges plyr reshape2 Rsamtools scales VariantAnnotation viridis]; }; GeneBreak = derive2 { name="GeneBreak"; version="1.30.0"; sha256="031i2z57hra21c52k4awdkzn6hg1dr31mb6360vq2br37nc07n04"; depends=[CGHbase CGHcall GenomicRanges QDNAseq]; }; GeneExpressionSignature = derive2 { name="GeneExpressionSignature"; version="1.46.0"; sha256="0lhrjzv26dffxmkixj5jn39rrxxvcjiams199qm56l30qsicx8xv"; depends=[Biobase]; }; + GeneGA = derive2 { name="GeneGA"; version="1.50.0"; sha256="1hzhrnl0i9h0ldbqb604wcdj93bnb6f4s7wz6llsa0266hzrkys7"; depends=[hash seqinr]; }; GeneGeneInteR = derive2 { name="GeneGeneInteR"; version="1.26.0"; sha256="1rpvan7m0lf9q5aix3di65hvdjkrssl3azs9ws5iiszsdmghs0fm"; depends=[data_table FactoMineR GenomicRanges igraph IRanges kernlab mvtnorm Rsamtools snpStats]; }; GeneMeta = derive2 { name="GeneMeta"; version="1.72.0"; sha256="07sj05wk8fbq0kdwvgm7rahp8mwri08cmlz2xcl44n85szv2mpji"; depends=[Biobase genefilter]; }; GeneNetworkBuilder = derive2 { name="GeneNetworkBuilder"; version="1.42.0"; sha256="0v6v6ij4cjbf1w0dvkfkw9qh0nsydd51rqmzaxcl0spry6r5z5zn"; depends=[graph htmlwidgets plyr Rcpp Rgraphviz rjson XML]; }; @@ -427,20 +428,20 @@ in with self; { GeneRegionScan = derive2 { name="GeneRegionScan"; version="1.56.0"; sha256="1z5qs7v9s6r72kmbkkv2krw89hnxg6lr0751jgyhkh2kwdh6k7va"; depends=[affxparser Biobase Biostrings RColorBrewer S4Vectors]; }; GeneSelectMMD = derive2 { name="GeneSelectMMD"; version="2.44.1"; sha256="0cx48dqdsry0a099f9s5yx1frbfnqsz9vrvdg2r8ika1inngzs8y"; depends=[Biobase limma MASS]; }; GeneStructureTools = derive2 { name="GeneStructureTools"; version="1.20.0"; sha256="04pln8ix4cmca3bq460b3rk57bj68rm3817mgpyh8l9425v6s0j6"; depends=[Biostrings BSgenome_Mmusculus_UCSC_mm10 data_table GenomicRanges Gviz IRanges plyr rtracklayer S4Vectors stringdist stringr]; }; - GeneTonic = derive2 { name="GeneTonic"; version="2.4.0"; sha256="0vk67mdn66gx5mz1i433aija0zbjqsw5am9xbbzkw3wi670bnc98"; depends=[AnnotationDbi backbone bs4Dash circlize colorspace colourpicker ComplexHeatmap ComplexUpset dendextend DESeq2 dplyr DT dynamicTreeCut expm ggforce ggplot2 ggrepel ggridges GO_db igraph matrixStats plotly RColorBrewer rintrojs rlang rmarkdown S4Vectors scales shiny shinyAce shinycssloaders shinyWidgets SummarizedExperiment tidyr tippy viridis visNetwork]; }; + GeneTonic = derive2 { name="GeneTonic"; version="2.4.2"; sha256="1vblvchpi83va0v0prgg4by9sxrni9jh8faq1b1kahy4bw9aa83x"; depends=[AnnotationDbi backbone bs4Dash circlize colorspace colourpicker ComplexHeatmap ComplexUpset dendextend DESeq2 dplyr DT dynamicTreeCut expm ggforce ggplot2 ggrepel ggridges GO_db igraph matrixStats plotly RColorBrewer rintrojs rlang rmarkdown S4Vectors scales shiny shinyAce shinycssloaders shinyWidgets SummarizedExperiment tidyr tippy viridis visNetwork]; }; GeneticsPed = derive2 { name="GeneticsPed"; version="1.62.1"; sha256="0620gg0hyz06n0843f72xy28a15h7dgx3s4mxj9x647ic82v4cm0"; depends=[gdata genetics MASS]; }; GenomAutomorphism = derive2 { name="GenomAutomorphism"; version="1.2.0"; sha256="0idffiapx9ycdaj5hpf50x5xhpgwb2a5gbfajmfrgw5g467qsqvp"; depends=[BiocGenerics BiocParallel Biostrings data_table doParallel dplyr foreach GenomeInfoDb GenomicRanges IRanges numbers S4Vectors]; }; - GenomeInfoDb = derive2 { name="GenomeInfoDb"; version="1.36.1"; sha256="1c3fgni846vjw152m4aklb8kwrwjw3rww116a2cbii70nr86p5qg"; depends=[BiocGenerics GenomeInfoDbData IRanges RCurl S4Vectors]; }; + GenomeInfoDb = derive2 { name="GenomeInfoDb"; version="1.36.4"; sha256="0wwh72sj894m3awk4g2zmkkwqafdjyxzsr49vnd1fiyz909hw02a"; depends=[BiocGenerics GenomeInfoDbData IRanges RCurl S4Vectors]; }; GenomicAlignments = derive2 { name="GenomicAlignments"; version="1.36.0"; sha256="1irzcz9s97gqbyj9j71wxv2ikdfd8g14296fg33w2ykfdm80nzf0"; depends=[BiocGenerics BiocParallel Biostrings GenomeInfoDb GenomicRanges IRanges Rsamtools S4Vectors SummarizedExperiment]; }; - GenomicDataCommons = derive2 { name="GenomicDataCommons"; version="1.24.2"; sha256="0dgvhi6nbc1qvrdwww2r39gxd2xmbadvy03lxh5nny9pyhhdlz3l"; depends=[dplyr GenomicRanges httr IRanges jsonlite magrittr rappdirs readr rlang tibble xml2]; }; + GenomicDataCommons = derive2 { name="GenomicDataCommons"; version="1.24.3"; sha256="1grvria7lx7p0py3w8yi0j41bpfx951lds5db7jdiq0j8l75fh38"; depends=[dplyr GenomicRanges httr IRanges jsonlite magrittr rappdirs readr rlang tibble tidyr xml2]; }; GenomicDistributions = derive2 { name="GenomicDistributions"; version="1.8.0"; sha256="1bxq7mqy8s9dcj1wsjzbrszvi1cfphvjbmxvb1pk1mxxa03zipjs"; depends=[Biostrings broom data_table dplyr GenomeInfoDb GenomicRanges ggplot2 IRanges plyr reshape2 scales]; }; - GenomicFeatures = derive2 { name="GenomicFeatures"; version="1.52.1"; sha256="166l0pzg00kaagg3adnx1xy5bgmv42lm06a47i30lh14dc0k79wq"; depends=[AnnotationDbi Biobase BiocGenerics BiocIO biomaRt Biostrings DBI GenomeInfoDb GenomicRanges IRanges RCurl RSQLite rtracklayer S4Vectors XVector]; }; + GenomicFeatures = derive2 { name="GenomicFeatures"; version="1.52.2"; sha256="0givyx77gvx24wgq180jsb2q1b8g4j49rs6bxdmd0l04a87hm9cr"; depends=[AnnotationDbi Biobase BiocGenerics BiocIO biomaRt Biostrings DBI GenomeInfoDb GenomicRanges IRanges RCurl RSQLite rtracklayer S4Vectors XVector]; }; GenomicFiles = derive2 { name="GenomicFiles"; version="1.36.0"; sha256="0nxz8lvpmyllgs1ksgbha8qqs4fhppkg5casppnas9x47dj4bxph"; depends=[BiocGenerics BiocParallel GenomeInfoDb GenomicAlignments GenomicRanges IRanges MatrixGenerics Rsamtools rtracklayer S4Vectors SummarizedExperiment VariantAnnotation]; }; GenomicInteractionNodes = derive2 { name="GenomicInteractionNodes"; version="1.4.0"; sha256="1wjlmydi74rsiqxg1pwz3f9zdc28p4xp4fa1lbjfskkd6b36d5p5"; depends=[AnnotationDbi GenomeInfoDb GenomicFeatures GenomicRanges GO_db graph IRanges RBGL S4Vectors]; }; GenomicInteractions = derive2 { name="GenomicInteractions"; version="1.34.0"; sha256="0qhb2mm5nynnw0cj5da0i6hb1bz7cyns0gp7xy0wscmfyh2wahbv"; depends=[Biobase BiocGenerics data_table dplyr GenomeInfoDb GenomicRanges ggplot2 gridExtra Gviz igraph InteractionSet IRanges Rsamtools rtracklayer S4Vectors stringr]; }; GenomicOZone = derive2 { name="GenomicOZone"; version="1.14.0"; sha256="0k4f22qnpwg227kxp68p93nx7q4gkkxd4d4z3dr104svgfidgq8k"; depends=[biomaRt Ckmeans_1d_dp GenomeInfoDb GenomicRanges ggbio ggplot2 gridExtra IRanges lsr plyr Rdpack S4Vectors]; }; - GenomicRanges = derive2 { name="GenomicRanges"; version="1.52.0"; sha256="0vbr8nqn4pk0w3wx94q4f44psy6lxgx4b7p8hp0vf46flwggj2lj"; depends=[BiocGenerics GenomeInfoDb IRanges S4Vectors XVector]; }; - GenomicScores = derive2 { name="GenomicScores"; version="2.12.0"; sha256="1z8h9sbr6xqwbsfisr33qdxg0xdrw8r4vvxl1pf4x8vv08zw0vx6"; depends=[AnnotationHub Biobase BiocFileCache BiocGenerics BiocManager Biostrings DelayedArray GenomeInfoDb GenomicRanges HDF5Array httr IRanges rhdf5 S4Vectors XML]; }; + GenomicRanges = derive2 { name="GenomicRanges"; version="1.52.1"; sha256="0n6b4kzyswhvakzvaql2x2j15r5ycx9ggvfmqq630m7xy3qzzrr0"; depends=[BiocGenerics GenomeInfoDb IRanges S4Vectors XVector]; }; + GenomicScores = derive2 { name="GenomicScores"; version="2.12.1"; sha256="1bs13aqb7yaz7bw6nscygpifcdn2dnkzkpqr2spvj2ws38lsahsz"; depends=[AnnotationHub Biobase BiocFileCache BiocGenerics BiocManager Biostrings DelayedArray GenomeInfoDb GenomicRanges HDF5Array httr IRanges rhdf5 S4Vectors XML]; }; GenomicSuperSignature = derive2 { name="GenomicSuperSignature"; version="1.8.0"; sha256="1wajx2r8dcscdgpz2dd1bdhpln258gpqs4bd4plq1ygjhnr2zbw4"; depends=[Biobase BiocFileCache ComplexHeatmap dplyr flextable ggplot2 ggpubr irlba plotly S4Vectors SummarizedExperiment]; }; GenomicTuples = derive2 { name="GenomicTuples"; version="1.34.0"; sha256="0yf64fjd0d8gspbdksv23j3ry4lab52j7kh7nizv944i387p2q13"; depends=[BiocGenerics data_table GenomeInfoDb GenomicRanges IRanges Rcpp S4Vectors]; }; GeoDiff = derive2 { name="GeoDiff"; version="1.6.0"; sha256="15d393xqc315wv98l08yfvxv866ciqccvqqx7zj0z8p2v2p5md18"; depends=[Biobase GeomxTools lme4 Matrix NanoStringNCTools plyr Rcpp RcppArmadillo robust roptim testthat withr]; }; @@ -453,15 +454,15 @@ in with self; { GraphAT = derive2 { name="GraphAT"; version="1.72.0"; sha256="0ibrlwf528687s5kk0hq72j9h8p5p18hrdx3823nr1s70vhysb3m"; depends=[graph MCMCpack]; }; GraphAlignment = derive2 { name="GraphAlignment"; version="1.64.0"; sha256="1zvmxrwbg72mjdr337azi2lbyaan7syndxqdz8xwas07jglgpycz"; depends=[]; }; GraphPAC = derive2 { name="GraphPAC"; version="1.42.0"; sha256="0rs71m850qsc9ickxkqlmcrwqsr66z7ji4mqgcg8kii0yjflpkvb"; depends=[igraph iPAC RMallow TSP]; }; - GreyListChIP = derive2 { name="GreyListChIP"; version="1.32.0"; sha256="1sfpf9msnzyrc8b0xzc2406bq2gkcwrrhv7fa9ynqv2ip6xwsc8s"; depends=[BSgenome GenomeInfoDb GenomicAlignments GenomicRanges MASS Rsamtools rtracklayer SummarizedExperiment]; }; + GreyListChIP = derive2 { name="GreyListChIP"; version="1.32.1"; sha256="0z89yikglx077x18qhq6f8f2fa9xni12jz8my9p5sa6zmvnj4dnm"; depends=[BSgenome GenomeInfoDb GenomicAlignments GenomicRanges MASS Rsamtools rtracklayer SummarizedExperiment]; }; Guitar = derive2 { name="Guitar"; version="2.16.0"; sha256="1v1yw90waq0ccj6pxdipipy5bnk0k762m5kadl4h3jgpcrkf2fvc"; depends=[AnnotationDbi dplyr GenomicFeatures GenomicRanges ggplot2 knitr magrittr rtracklayer]; }; - Gviz = derive2 { name="Gviz"; version="1.44.0"; sha256="1lp345hxlddsc91lxrzay073g2dabc8h1cynyh87y85vzffhwplw"; depends=[AnnotationDbi Biobase BiocGenerics biomaRt Biostrings biovizBase BSgenome digest ensembldb GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges lattice latticeExtra matrixStats RColorBrewer Rsamtools rtracklayer S4Vectors XVector]; }; + Gviz = derive2 { name="Gviz"; version="1.44.2"; sha256="0laismy8kklzkg81r5vf1194fbhp2hw952g6jc3zvn2z5y2d4524"; depends=[AnnotationDbi Biobase BiocGenerics biomaRt Biostrings biovizBase BSgenome digest ensembldb GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges lattice latticeExtra matrixStats RColorBrewer Rsamtools rtracklayer S4Vectors XVector]; }; HDF5Array = derive2 { name="HDF5Array"; version="1.28.1"; sha256="1riwxxnbi4z0lf42psh3m3ivxlgmmlnqhgsih6911c754r6s39qg"; depends=[BiocGenerics DelayedArray IRanges Matrix rhdf5 rhdf5filters Rhdf5lib S4Arrays S4Vectors]; }; HDTD = derive2 { name="HDTD"; version="1.34.1"; sha256="0gyav2g5c7gphqxbj6mr96g06nr1n5jrn8dkidr8l4ripv5ycx59"; depends=[Rcpp RcppArmadillo]; }; HELP = derive2 { name="HELP"; version="1.58.0"; sha256="1bhyjk2cmyw2s51s474ccykjrja3m3gv6jzdmv7a4zkcfa7fa7wg"; depends=[Biobase]; }; HEM = derive2 { name="HEM"; version="1.72.0"; sha256="0b5pc1ybml1wk406s1b4pbarcayc9nyf0cvqvr28g7rr8q88kgsq"; depends=[Biobase]; }; HGC = derive2 { name="HGC"; version="1.8.0"; sha256="1kjhiw6g3an2yvb709idwkhwq8lw27r7d4g2kb5l5b77b0rr81hz"; depends=[ape dendextend dplyr ggplot2 Matrix mclust patchwork RANN Rcpp RcppEigen]; }; - HIBAG = derive2 { name="HIBAG"; version="1.36.1"; sha256="181xdz6hlfbq765ljj61nxj6nzzmj4675v1zw5qr9nwg58xwjv82"; depends=[RcppParallel]; }; + HIBAG = derive2 { name="HIBAG"; version="1.36.4"; sha256="1cck7d7966b2plbqv1sdp6s32nvigi67s0cwmgb1rnqq0jakhp4a"; depends=[RcppParallel]; }; HIPPO = derive2 { name="HIPPO"; version="1.12.0"; sha256="0lhs56r6wlg586xl18wxzhg8q8mhcm7qd7rjgx4hk50xa9c16cxz"; depends=[dplyr ggplot2 ggrepel gridExtra irlba magrittr Matrix reshape2 rlang Rtsne SingleCellExperiment umap]; }; HIREewas = derive2 { name="HIREewas"; version="1.18.0"; sha256="0p0mcb5n6y4zw0df2a5irzwg3wmdk8vgp2hvrjr9vswbma8jxxfa"; depends=[gplots quadprog]; }; HMMcopy = derive2 { name="HMMcopy"; version="1.42.0"; sha256="0vvg7jy38q43v9nvp18h6lhjkkcqgrgzgnhkb1v1fm03g5kg3fi6"; depends=[data_table]; }; @@ -488,8 +489,8 @@ in with self; { HilbertCurve = derive2 { name="HilbertCurve"; version="1.30.0"; sha256="160n5lrghqhsm69qhgbhi1g018i6f7wqr1rp9mlvy4mqndzygdnp"; depends=[circlize GenomicRanges HilbertVis IRanges png polylabelr]; }; HilbertVis = derive2 { name="HilbertVis"; version="1.58.0"; sha256="12gzfnkkxhw9nyha70ghh8vqp7283grif0aahw3413xzppb2v3bh"; depends=[lattice]; }; HilbertVisGUI = derive2 { name="HilbertVisGUI"; version="1.58.0"; sha256="166vk1pysxldkqwpi76x5vppw09d75kdqclkizpnx149wf5lxx2f"; depends=[HilbertVis]; }; - HubPub = derive2 { name="HubPub"; version="1.8.0"; sha256="0v2ipm2351z7829rg3icfgci3g8jrjmh94j6d5njfskpl71aihh5"; depends=[available aws_s3 BiocManager biocthis dplyr fs usethis]; }; - HumanTranscriptomeCompendium = derive2 { name="HumanTranscriptomeCompendium"; version="1.16.0"; sha256="11pfnpjga1rxs7mjc2jk72si8z2vgk0yhc0hiy4cvfiw653pwzzg"; depends=[S4Vectors shiny ssrch SummarizedExperiment]; }; + HubPub = derive2 { name="HubPub"; version="1.8.1"; sha256="07dz4a40g5dfvys3vrw9fk0b6knypg0gqgari7bgvqnghx500vvb"; depends=[available aws_s3 BiocManager biocthis dplyr fs usethis]; }; + HumanTranscriptomeCompendium = derive2 { name="HumanTranscriptomeCompendium"; version="1.16.3"; sha256="0fiw4r4dix4683w61292micdgp65i90s4hxfx69zm667zjk0b5r8"; depends=[BiocManager S4Vectors shiny ssrch SummarizedExperiment]; }; HybridMTest = derive2 { name="HybridMTest"; version="1.44.0"; sha256="19pycad35hc7ylnsz75bv029y1r6j9xvrbhzk4i64i7jn8gi7ngh"; depends=[Biobase fdrtool MASS survival]; }; IFAA = derive2 { name="IFAA"; version="1.2.0"; sha256="1bvx78akdyr4wcghjq2j035bzir6aas6wydmmbpv72whpcvpqpdk"; depends=[DescTools doParallel doRNG foreach glmnet HDCI mathjaxr Matrix MatrixExtra parallelly S4Vectors stringr SummarizedExperiment]; }; IHW = derive2 { name="IHW"; version="1.28.0"; sha256="0i4yahgkrg9rnc0xldm026k6bd1bn5nkgkaf6kpyyday41rxzyq8"; depends=[BiocGenerics fdrtool lpsymphony slam]; }; @@ -530,7 +531,7 @@ in with self; { IsoformSwitchAnalyzeR = derive2 { name="IsoformSwitchAnalyzeR"; version="2.0.1"; sha256="1zjwhxlayz2sb77vspw280didhawj282i5gvxnydcdparg165zwf"; depends=[Biobase BiocGenerics BiocParallel Biostrings BSgenome DBI DEXSeq dplyr edgeR futile_logger GenomeInfoDb GenomicRanges ggplot2 gridExtra IRanges limma magrittr pfamAnalyzeR plyr RColorBrewer RCurl readr reshape2 rtracklayer S4Vectors satuRn stringr SummarizedExperiment sva tibble tidyr tximeta tximport VennDiagram XVector]; }; KBoost = derive2 { name="KBoost"; version="1.8.0"; sha256="1gisi1s2q1qjr8lfbkpa717s8x8idssdv12nic5h2r82v1pdhmzd"; depends=[]; }; KCsmart = derive2 { name="KCsmart"; version="2.58.0"; sha256="0sv7q7fx7wwin1hcba4izb75vrc2n02ig0rq17zdb8x8z14wbndb"; depends=[BiocGenerics KernSmooth multtest siggenes]; }; - KEGGREST = derive2 { name="KEGGREST"; version="1.40.0"; sha256="1zmsk5w8i3cq0983nx1d24a6awrbq7aj2wrapsnizq9gvrsrhbbb"; depends=[Biostrings httr png]; }; + KEGGREST = derive2 { name="KEGGREST"; version="1.40.1"; sha256="13pbw5nlkjwplliv2pdwazv2idfjklvw0ykx5ja8rchvzs5f1vk4"; depends=[Biostrings httr png]; }; KEGGgraph = derive2 { name="KEGGgraph"; version="1.60.0"; sha256="0bgigkmnz5zvsygcifk2fc7i8rahmqr4brk65qa3104clqqvdfkl"; depends=[graph RCurl Rgraphviz XML]; }; KEGGlincs = derive2 { name="KEGGlincs"; version="1.26.0"; sha256="0s8d2sw54k4m5s1yi7mijbc3hh7wayi5npgh8z7xiqj49mzali01"; depends=[AnnotationDbi gtools hgu133a_db httr igraph KEGGgraph KEGGREST KOdata org_Hs_eg_db plyr RJSONIO XML]; }; KinSwingR = derive2 { name="KinSwingR"; version="1.18.0"; sha256="0ibwcdx2h6y80fhf5ln7rw6b9gfcpkr09vdypcnlfvz4nzr3x9k8"; depends=[BiocParallel data_table sqldf]; }; @@ -607,7 +608,7 @@ in with self; { MSstatsQC = derive2 { name="MSstatsQC"; version="2.18.0"; sha256="1b5hy55wa34lkj5gr1jvirgjy8nk0ym6rpkvkap51b7z59dfsbn8"; depends=[dplyr ggExtra ggplot2 MSnbase plotly qcmetrics]; }; MSstatsQCgui = derive2 { name="MSstatsQCgui"; version="1.20.0"; sha256="1jj3ji8k66x3fnvz67b2ssr7jvm1j1plnpircwhk6vska0yy5jdc"; depends=[dplyr ggExtra gridExtra MSstatsQC plotly shiny]; }; MSstatsSampleSize = derive2 { name="MSstatsSampleSize"; version="1.13.0"; sha256="09gmlqxb65pa4wxh5bryb6lhs68zrfaqfl7n3k9shvzi3iw02vp3"; depends=[BiocParallel caret ggplot2 gridExtra MSstats reshape2]; }; - MSstatsShiny = derive2 { name="MSstatsShiny"; version="1.2.4"; sha256="07hyrjf81qacmmzirijqd1nnw7i8f8p9iglpxinyvcz1qm4hyd27"; depends=[data_table dplyr DT ggplot2 ggrepel gplots Hmisc htmltools marray MSstats MSstatsConvert MSstatsPTM MSstatsTMT readxl shiny shinyBS shinybusy shinyjs tidyr uuid]; }; + MSstatsShiny = derive2 { name="MSstatsShiny"; version="1.2.5"; sha256="067nnbdmip7g4vp8jl29k1wjql3misnqjzs3hxva8wsscdvf6hd0"; depends=[data_table dplyr DT ggplot2 ggrepel gplots Hmisc htmltools marray MSstats MSstatsConvert MSstatsPTM MSstatsTMT readxl shiny shinyBS shinybusy shinyjs tidyr uuid]; }; MSstatsTMT = derive2 { name="MSstatsTMT"; version="2.8.0"; sha256="0n4dc178b1wdb3w0i5hr0zdm6ijcyn7ir8rjaalpz3aq5dkvslc9"; depends=[checkmate data_table ggplot2 limma lme4 lmerTest MSstats MSstatsConvert]; }; MVCClass = derive2 { name="MVCClass"; version="1.74.0"; sha256="1vrn2c5m4w7g13s1zd1am5b02lp026zg6gvpg8dvsras0j56rhr6"; depends=[]; }; MWASTools = derive2 { name="MWASTools"; version="1.24.0"; sha256="0klyclh5hiiwc9lc2ra3d2gcdl58jmda0xd9h499gv94mzhb6d50"; depends=[boot car ComplexHeatmap ggplot2 glm2 gridExtra igraph KEGGgraph KEGGREST ppcor qvalue RCurl SummarizedExperiment]; }; @@ -632,9 +633,9 @@ in with self; { MetaPhOR = derive2 { name="MetaPhOR"; version="1.2.0"; sha256="1dhldl6vxp12rsbk9sdklb5r8gyi4fybfbfkxs5cb3y1ygq83vcd"; depends=[clusterProfiler ggplot2 ggrepel pheatmap RCy3 RecordLinkage stringr]; }; MetaVolcanoR = derive2 { name="MetaVolcanoR"; version="1.14.0"; sha256="11fxjv0kb65wc2237rh3340j72v3zsd4s019bi07rbpqnl246pnj"; depends=[cowplot data_table dplyr ggplot2 htmlwidgets metafor metap plotly rlang tidyr topconfects]; }; Metab = derive2 { name="Metab"; version="1.33.0"; sha256="0fid4b3yk56z2sm6hxfp0z30nqjsky9sv4x49x912bw61amvrwky"; depends=[pander svDialogs xcms]; }; - MetaboAnnotation = derive2 { name="MetaboAnnotation"; version="1.4.1"; sha256="0kr6457ymbf44m4dwhyq8n6b49rnp986zdl4gpdmvb634s86ghcm"; depends=[BiocGenerics BiocParallel CompoundDb MetaboCoreUtils MsCoreUtils ProtGenerics QFeatures S4Vectors Spectra SummarizedExperiment]; }; + MetaboAnnotation = derive2 { name="MetaboAnnotation"; version="1.4.3"; sha256="1n82zfkjm06brn8hzydx4q2qwxdaygbc436hjg0bqk0q905d8s4j"; depends=[AnnotationHub BiocGenerics BiocParallel CompoundDb MetaboCoreUtils MsCoreUtils ProtGenerics QFeatures S4Vectors Spectra SummarizedExperiment]; }; MetaboCoreUtils = derive2 { name="MetaboCoreUtils"; version="1.8.0"; sha256="1qg66w0fxhxfp6yx6jgplj0vd4gvfwa95hr4516cdjzzwcc1xaqb"; depends=[MsCoreUtils]; }; - MetaboSignal = derive2 { name="MetaboSignal"; version="1.30.2"; sha256="0f7yr2cq4vghzlczmaqhrwfa7idaqjjaxi02s298mmkwn9wkq9m7"; depends=[AnnotationDbi biomaRt EnsDb_Hsapiens_v75 hpar igraph KEGGgraph KEGGREST MWASTools mygene org_Hs_eg_db RCurl]; }; + MetaboSignal = derive2 { name="MetaboSignal"; version="1.30.3"; sha256="1xm3lkjs1i2cwsl60699nnrq50j1dfhc3799v44rr0sjzzhqr87h"; depends=[AnnotationDbi biomaRt EnsDb_Hsapiens_v75 hpar igraph KEGGgraph KEGGREST MWASTools mygene org_Hs_eg_db RCurl]; }; MethPed = derive2 { name="MethPed"; version="1.28.0"; sha256="1gp1y9h6rkrvj0xbi915lsq5b6gvgyydq8l012pf6nm1dq8xwgzj"; depends=[Biobase randomForest]; }; MethReg = derive2 { name="MethReg"; version="1.10.2"; sha256="085vd6wymahnvbvj4lj21iq2zpn42jv1w6a46mfa6lhban6s0xx5"; depends=[AnnotationHub DelayedArray dplyr ExperimentHub GenomicRanges ggplot2 ggpubr IRanges MASS Matrix plyr progress pscl readr rlang S4Vectors sesame sesameData sfsmisc stringr SummarizedExperiment tibble tidyr]; }; MethTargetedNGS = derive2 { name="MethTargetedNGS"; version="1.32.0"; sha256="05yl7z8fx6p2zzr2vkm7dvyxxcvr52w3hxfgs045w1klpsnrvsr3"; depends=[Biostrings gplots seqinr stringr]; }; @@ -646,13 +647,13 @@ in with self; { MiPP = derive2 { name="MiPP"; version="1.72.0"; sha256="1ifh4961092zw89rl45iirhrpmz2629avr54lqrkf748ph5icprv"; depends=[Biobase e1071 MASS]; }; MiRaGE = derive2 { name="MiRaGE"; version="1.42.0"; sha256="0yry5n4gk46f4b7s5zd0nha782h8a72510javbb9law5iahch2ag"; depends=[AnnotationDbi Biobase BiocGenerics BiocManager S4Vectors]; }; MicrobiomeProfiler = derive2 { name="MicrobiomeProfiler"; version="1.6.1"; sha256="1hp9q3nyza6pvdgr79kp2vc91xmr5qnpx3650gxa2y9c8jkcf5ln"; depends=[clusterProfiler config DT enrichplot ggplot2 golem gson htmltools magrittr shiny shinycustomloader shinyWidgets]; }; - MicrobiotaProcess = derive2 { name="MicrobiotaProcess"; version="1.12.3"; sha256="1dpw86762waj48qxa9sbn6klz2nj6hlbqn0ra9jay7gkfb8sybp7"; depends=[ape Biostrings cli coin data_table dplyr dtplyr foreach ggfun ggplot2 ggrepel ggsignif ggstar ggtree ggtreeExtra magrittr MASS patchwork pillar plyr rlang SummarizedExperiment tibble tidyr tidyselect tidytree treeio vegan zoo]; }; + MicrobiotaProcess = derive2 { name="MicrobiotaProcess"; version="1.12.4"; sha256="1yl9vg8j9x66jnkp2s823rpvpn0qrlzmc01fzw9zj5f2kzsw5238"; depends=[ape Biostrings cli coin data_table dplyr dtplyr foreach ggfun ggplot2 ggrepel ggsignif ggstar ggtree ggtreeExtra magrittr MASS patchwork pillar plyr rlang SummarizedExperiment tibble tidyr tidyselect tidytree treeio vegan zoo]; }; MineICA = derive2 { name="MineICA"; version="1.40.0"; sha256="0vpjf2vjg9hk1j39c5f37m2rvpspwnygs4yax4gp9i3iwvsrsf4a"; depends=[annotate AnnotationDbi Biobase BiocGenerics biomaRt cluster colorspace fastICA foreach fpc ggplot2 GOstats graph gtools Hmisc igraph JADE lumi lumiHumanAll_db marray mclust plyr RColorBrewer Rgraphviz scales xtable]; }; MinimumDistance = derive2 { name="MinimumDistance"; version="1.44.0"; sha256="1axlwnws57ldlphifd30a9hzxjhsxbjrg5k0h7lxhmrrby1cf62d"; depends=[Biobase BiocGenerics data_table DNAcopy ff foreach GenomeInfoDb GenomicRanges IRanges lattice MatrixGenerics matrixStats oligoClasses S4Vectors SummarizedExperiment VanillaICE]; }; MobilityTransformR = derive2 { name="MobilityTransformR"; version="1.4.0"; sha256="0dwshk5azfrvajalyjr2l8l8cfls3070p3jqk1s2j6ni85p7qxbb"; depends=[MetaboCoreUtils MSnbase Spectra xcms]; }; ModCon = derive2 { name="ModCon"; version="1.8.0"; sha256="1vr8v88cgb7c8svghc13b8a4j4gfq77y2p8px7y0bhm3zlx97ay0"; depends=[data_table]; }; Modstrings = derive2 { name="Modstrings"; version="1.16.0"; sha256="1q0qmcnyblnjkxnis1klgmd2zy226jr9iwwqzvrrbqs1wxpd4ap9"; depends=[BiocGenerics Biostrings crayon GenomicRanges IRanges S4Vectors stringi stringr XVector]; }; - MoleculeExperiment = derive2 { name="MoleculeExperiment"; version="1.0.2"; sha256="1n7hvis542a98a5lxj3w2x09cigrnpmg76132dk3b518vhacxl37"; depends=[BiocParallel cli data_table dplyr EBImage ggplot2 magrittr Matrix purrr rhdf5 rjson rlang SpatialExperiment terra]; }; + MoleculeExperiment = derive2 { name="MoleculeExperiment"; version="1.0.3"; sha256="01x2wmkpd23fkx021fz96yhq26hhqr3p4f5bsshxmzmhqxcw89l9"; depends=[BiocParallel cli data_table dplyr EBImage ggplot2 magrittr Matrix purrr rhdf5 rjson rlang S4Vectors SpatialExperiment terra]; }; MoonlightR = derive2 { name="MoonlightR"; version="1.26.1"; sha256="1p9cnq07qmybqz0qqrcka5cvbm9bd68q5k0pn35wkysmk2jakdhq"; depends=[Biobase circlize clusterProfiler doParallel DOSE foreach GEOquery gplots HiveR limma parmigene randomForest RColorBrewer RISmed SummarizedExperiment TCGAbiolinks]; }; Motif2Site = derive2 { name="Motif2Site"; version="1.4.0"; sha256="1paw91v8f7gf3p18kwjzxjjhqgfsyf3hgw0ppbmmp71ix4jpqirj"; depends=[BiocGenerics Biostrings BSgenome edgeR GenomeInfoDb GenomicAlignments GenomicRanges IRanges MASS mixtools S4Vectors]; }; MotifDb = derive2 { name="MotifDb"; version="1.42.0"; sha256="18d0qj9sn4bhfjy2mwsz2nnm41xlsqjslsv69nkhv19w9zd842pw"; depends=[BiocGenerics Biostrings GenomicRanges IRanges rtracklayer S4Vectors splitstackshape]; }; @@ -678,7 +679,7 @@ in with self; { MutationalPatterns = derive2 { name="MutationalPatterns"; version="3.10.0"; sha256="1p9n5afnr4cx690w9d5q1hkwqffsbnsn72wibqcl5rbqgfsvhf8h"; depends=[BiocGenerics Biostrings BSgenome cowplot dplyr GenomeInfoDb GenomicRanges ggalluvial ggdendro ggplot2 IRanges magrittr NMF pracma purrr RColorBrewer S4Vectors stringr tibble tidyr VariantAnnotation]; }; NADfinder = derive2 { name="NADfinder"; version="1.24.0"; sha256="0fc7z12hwjxfcyx9pqfwzjb4s3ijr6gnm4bnz9fsr13nncl9p3rr"; depends=[ATACseqQC baseline BiocGenerics corrplot csaw EmpiricalBrownsMethod GenomeInfoDb GenomicAlignments GenomicRanges IRanges limma metap Rsamtools rtracklayer S4Vectors signal SummarizedExperiment trackViewer]; }; NBAMSeq = derive2 { name="NBAMSeq"; version="1.16.0"; sha256="1l5mk5mdbqypljrnnl7zcz8mgixg44bxaflka8wkfc60757qqkbd"; depends=[BiocParallel DESeq2 genefilter mgcv S4Vectors SummarizedExperiment]; }; - NCIgraph = derive2 { name="NCIgraph"; version="1.48.0"; sha256="0spzrf72y34vi0c9biz37b7id087928bf3qf9sxp9gybfdk6jp7n"; depends=[graph KEGGgraph R_methodsS3 RBGL RCy3]; }; + NCIgraph = derive2 { name="NCIgraph"; version="1.48.1"; sha256="0q7a4x50fkwi80lqdsfyr4nqa97xzld7n0lihpvr3zi44hcs9a1w"; depends=[graph KEGGgraph R_oo RBGL RCy3]; }; NOISeq = derive2 { name="NOISeq"; version="2.44.0"; sha256="0cxhy4yrww6bh4z603389fikhix8rhfy04ylhm74fdmdng4jblg6"; depends=[Biobase Matrix]; }; NPARC = derive2 { name="NPARC"; version="1.12.0"; sha256="1dx585zs94zazqy9hbrhivpn6p76a68nvlg6vng2r1qqmm2685mc"; depends=[BiocParallel broom dplyr magrittr MASS rlang tidyr]; }; NTW = derive2 { name="NTW"; version="1.50.0"; sha256="1vmqd9jbjpjni5511fzvgkg2q22nxadm3a7xs97n8fc8w9jyghmc"; depends=[mvtnorm]; }; @@ -693,8 +694,9 @@ in with self; { NetPathMiner = derive2 { name="NetPathMiner"; version="1.36.0"; sha256="0fbi4gbjxxxw76b9fph7gc6mqa4lyvsn5vwhfxwy50divl1w1i1r"; depends=[igraph]; }; NetSAM = derive2 { name="NetSAM"; version="1.40.0"; sha256="056fz9zipamxq1rhrvk80yph5rvv2sackyxsbaxjpcafscj8j4gn"; depends=[AnnotationDbi biomaRt DBI doParallel foreach GO_db igraph R2HTML seriation survival WGCNA]; }; NeuCA = derive2 { name="NeuCA"; version="1.6.0"; sha256="01bbmgmj873r3kjvsh8p1v9jzdhfzpn2rlq29bv1xf9hfvljm0ka"; depends=[e1071 keras limma SingleCellExperiment]; }; + NewWave = derive2 { name="NewWave"; version="1.10.0"; sha256="0ndy9d2xv166yxyqjzjs9y2mi214qdqm99pzydpn5xqyg72ljid5"; depends=[BiocSingular DelayedArray irlba Matrix SharedObject SingleCellExperiment SummarizedExperiment]; }; NoRCE = derive2 { name="NoRCE"; version="1.12.0"; sha256="03pb0k638v56sws8ic92r6bq4kmr3rq9n4zhk32bmzbcnxyf4zc2"; depends=[AnnotationDbi biomaRt DBI dbplyr dplyr GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 GO_db igraph IRanges KEGGREST png RCurl reactome_db readr reshape2 RSQLite rtracklayer rWikiPathways S4Vectors stringr SummarizedExperiment tidyr zlibbioc]; }; - NormalyzerDE = derive2 { name="NormalyzerDE"; version="1.18.0"; sha256="1vip8r8588m3zcg7d49jmnacbdhh0nc0inga222v5qs4kpcr3z5k"; depends=[ape Biobase car ggforce ggplot2 limma MASS matrixStats preprocessCore raster RcmdrMisc SummarizedExperiment vsn]; }; + NormalyzerDE = derive2 { name="NormalyzerDE"; version="1.18.1"; sha256="0vdj7fd8nnm0xdjmfd9hrmnwspm0qzxgzsnr7bm4frr989z92xrs"; depends=[ape Biobase car ggforce ggplot2 limma MASS matrixStats preprocessCore raster RcmdrMisc SummarizedExperiment vsn]; }; NormqPCR = derive2 { name="NormqPCR"; version="1.46.0"; sha256="1fq9f7q4nslls46pgf1x82karwk8kf89si5mgdbi6a73k672d0dk"; depends=[Biobase qpcR RColorBrewer ReadqPCR]; }; NuPoP = derive2 { name="NuPoP"; version="2.8.1"; sha256="1nv88nrh1gmambcdm6xvpm8zjn4qg9hq0hbpz13p624zi364qyji"; depends=[]; }; NxtIRFcore = derive2 { name="NxtIRFcore"; version="1.6.0"; sha256="1x3645v6ar8mpmyk6hd5w3m38496g68l2vdh80vh0hhlqlrp17n2"; depends=[AnnotationHub BiocFileCache BiocGenerics BiocParallel Biostrings BSgenome data_table DelayedArray DelayedMatrixStats fst genefilter GenomeInfoDb GenomicRanges ggplot2 HDF5Array IRanges magrittr NxtIRFdata plotly R_utils Rcpp RcppProgress rhdf5 rtracklayer S4Vectors SummarizedExperiment zlibbioc]; }; @@ -706,7 +708,7 @@ in with self; { OMICsPCA = derive2 { name="OMICsPCA"; version="1.18.0"; sha256="1rkzs0i1650pz9q8v6axwspd3ykvmjd95zcbrgglm2r1gxw1iihn"; depends=[cluster clValid corrplot cowplot data_table factoextra FactoMineR fpc GenomeInfoDb ggplot2 HelloRanges IRanges kableExtra magick MASS MultiAssayExperiment NbClust OMICsPCAdata pdftools PerformanceAnalytics reshape2 rgl rmarkdown rtracklayer tidyr]; }; OPWeight = derive2 { name="OPWeight"; version="1.22.0"; sha256="0fklx2c0p7h23976ywh74xsz3p55j5jq83qvqipynpxkp8b1jv7h"; depends=[MASS qvalue tibble]; }; ORFhunteR = derive2 { name="ORFhunteR"; version="1.8.0"; sha256="03b4lz466hflprn6w3j6p0xrq9prrxd390zmn98v09819w9spl0i"; depends=[Biostrings BSgenome_Hsapiens_UCSC_hg38 data_table Peptides randomForest Rcpp rtracklayer stringr xfun]; }; - ORFik = derive2 { name="ORFik"; version="1.20.1"; sha256="0vwi84nyfp3gdrnbgbz8m2896wb7xg7ima6hkcbwddxvwa209wrs"; depends=[AnnotationDbi BiocGenerics BiocParallel biomaRt biomartr Biostrings BSgenome cowplot curl data_table DESeq2 downloader dplyr fst GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 gridExtra httr IRanges jsonlite R_utils Rcpp RCurl readr Rsamtools rtracklayer S4Vectors stringr SummarizedExperiment tibble withr XML xml2]; }; + ORFik = derive2 { name="ORFik"; version="1.20.2"; sha256="1qdgi10za2d6mvqixx05fyr21blm8qmlpamir9mw9hhgjpvky7l9"; depends=[AnnotationDbi BiocGenerics BiocParallel biomaRt biomartr Biostrings BSgenome cowplot curl data_table DESeq2 downloader dplyr fst GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 gridExtra httr IRanges jsonlite R_utils Rcpp RCurl readr Rsamtools rtracklayer S4Vectors stringr SummarizedExperiment tibble withr XML xml2]; }; OSAT = derive2 { name="OSAT"; version="1.48.0"; sha256="095zbj204z705ai1fzj70m316ihg04f93cvjyx64wk5pbqdg5p4d"; depends=[]; }; OTUbase = derive2 { name="OTUbase"; version="1.50.0"; sha256="0n2fghi0b5f012l57lr4qsvj85kjsg80iqpsgfajkdakam860i3w"; depends=[Biobase Biostrings IRanges S4Vectors ShortRead vegan]; }; OUTRIDER = derive2 { name="OUTRIDER"; version="1.18.1"; sha256="08xkpsqpgg9xjz9lalsxxvfyqjljby6q5i8awv5m2c8zn5b0mami"; depends=[BBmisc BiocGenerics BiocParallel data_table DESeq2 generics GenomicFeatures GenomicRanges ggplot2 heatmaply IRanges matrixStats pcaMethods pheatmap plotly plyr PRROC RColorBrewer Rcpp RcppArmadillo reshape2 S4Vectors scales SummarizedExperiment]; }; @@ -715,7 +717,7 @@ in with self; { OmicCircos = derive2 { name="OmicCircos"; version="1.38.0"; sha256="0zqw0ccngkh00l5wk2kn6fpr249rrkm8sasrzypax943xygnh6i0"; depends=[GenomicRanges]; }; OmicsLonDA = derive2 { name="OmicsLonDA"; version="1.15.0"; sha256="1kn26k0lnk7hgfzk1kh5bh41zkia8a4pzsfr35mbjrflcxmvgk2w"; depends=[BiocGenerics BiocParallel ggplot2 gss plyr pracma SummarizedExperiment zoo]; }; Omixer = derive2 { name="Omixer"; version="1.10.0"; sha256="0piqs23sdsphsynv2wqs7vmpjgsl1kymfjr3xx9nx9jrzjhh5fma"; depends=[dplyr forcats ggplot2 gridExtra magrittr readr stringr tibble tidyselect]; }; - OmnipathR = derive2 { name="OmnipathR"; version="3.8.0"; sha256="0r2nv3nbadnvqby7p5bdpl9fxjb30h0c8kjv1dkqqnhk5rbfl4hf"; depends=[checkmate crayon curl digest dplyr httr igraph jsonlite later logger magrittr progress purrr rappdirs readr readxl rlang rmarkdown rvest stringr tibble tidyr tidyselect withr xml2 yaml]; }; + OmnipathR = derive2 { name="OmnipathR"; version="3.8.2"; sha256="13ac98jj03vkzrc1ghrs98qrfvr74wz099w26lgc7jw2yxj575as"; depends=[checkmate crayon curl digest dplyr httr igraph jsonlite later logger magrittr progress purrr rappdirs readr readxl rlang rmarkdown rvest stringr tibble tidyr tidyselect withr xml2 yaml]; }; OncoScore = derive2 { name="OncoScore"; version="1.28.0"; sha256="00wnw7b9sj00h6kdlbh9r8frdcy8x5vdxjc8v2cbk6avll8w2z9a"; depends=[biomaRt]; }; OncoSimulR = derive2 { name="OncoSimulR"; version="4.2.0"; sha256="1s33kjsv72zslygg108m16wrzv4d55xn0pdjfpzy9sdgh2j8yviz"; depends=[car data_table dplyr ggplot2 ggrepel graph gtools igraph RColorBrewer Rcpp Rgraphviz smatr stringr]; }; OpenStats = derive2 { name="OpenStats"; version="1.12.0"; sha256="1pw6g4nrnmvfd5qbg3z79qzlzyf0n196vpklx8xwhd7zpr6djbkq"; depends=[AICcmodavg car Hmisc jsonlite knitr MASS nlme rlist summarytools]; }; @@ -761,13 +763,13 @@ in with self; { PhenStat = derive2 { name="PhenStat"; version="2.36.0"; sha256="1q5lpn352acpzfawwch0n4dra3znb7rghg4zl7wnc146s6628pyd"; depends=[car corrplot ggplot2 graph knitr lme4 logistf MASS msgps nlme nortest pingr reshape SmoothWin]; }; PhenoGeneRanker = derive2 { name="PhenoGeneRanker"; version="1.8.0"; sha256="1izqzvasir1jsfas626m82141gd34zk6j0k4ff4n2dk4r51id37n"; depends=[doParallel dplyr foreach igraph Matrix]; }; PhosR = derive2 { name="PhosR"; version="1.10.0"; sha256="0lcri7cfx2bvva1c48bq7rqzk9vag0rqy00myxhy3nqqp5vf16ws"; depends=[BiocGenerics circlize dendextend dplyr e1071 GGally ggdendro ggplot2 ggpubr ggtext igraph limma network pcaMethods pheatmap preprocessCore RColorBrewer reshape2 rlang ruv S4Vectors stringi SummarizedExperiment tidyr]; }; - PhyloProfile = derive2 { name="PhyloProfile"; version="1.14.5"; sha256="1vxlh59h08n3qn3mq3ry82j89il72dbl6j1qbwxzmgick0fn9d5p"; depends=[ape BiocStyle bioDist Biostrings colourpicker data_table DT energy ExperimentHub ggplot2 gridExtra OmaDB pbapply plyr RColorBrewer RCurl shiny shinyBS shinyFiles shinyjs xml2 yaml zoo]; }; + PhyloProfile = derive2 { name="PhyloProfile"; version="1.14.6"; sha256="1kgxani11748n4jglfh58p2v7sj8q42sql4fl07hgnbcpb0amg5x"; depends=[ape BiocStyle bioDist Biostrings colourpicker data_table DT energy ExperimentHub ggplot2 gridExtra OmaDB pbapply plyr RColorBrewer RCurl shiny shinyBS shinyFiles shinyjs xml2 yaml zoo]; }; Pi = derive2 { name="Pi"; version="2.12.0"; sha256="1k6i2byxranyph1034aph1vr1jjkx4d9gsni666p60ssg05bbvbi"; depends=[BiocGenerics caret dnet dplyr GenomeInfoDb GenomicRanges ggnetwork ggplot2 ggrepel glmnet igraph IRanges lattice MASS Matrix osfr plot3D purrr randomForest RCircos readr ROCR scales supraHex tibble tidyr]; }; Pigengene = derive2 { name="Pigengene"; version="1.26.0"; sha256="0b13bkj554w1wh6z393lw6l2ndydkblx4pck7zl0vbh2mwiiamkm"; depends=[BiocStyle bnlearn C50 clusterProfiler DBI DOSE dplyr gdata ggplot2 GO_db graph impute MASS matrixStats openxlsx partykit pheatmap preprocessCore ReactomePA Rgraphviz WGCNA]; }; PloGO2 = derive2 { name="PloGO2"; version="1.12.0"; sha256="1s5ay04ky0bimn4kqzqakygldcd08s7d0kvbn6sdyhf39avb6vv3"; depends=[GO_db GOstats httr lattice openxlsx xtable]; }; PoDCall = derive2 { name="PoDCall"; version="1.8.0"; sha256="1vph2lvs0wcnx56yngzw7ms2si8zq1k4imxrixzhvs0xj67qkbfc"; depends=[diptest DT ggplot2 gridExtra LaplacesDemon mclust purrr readr rlist shiny shinyjs]; }; PrInCE = derive2 { name="PrInCE"; version="1.16.0"; sha256="012dnavlx0abizh7bfms8cn4c4hx3sps3hzivddskap5czi7drxv"; depends=[Biobase dplyr forecast Hmisc LiblineaR magrittr MSnbase naivebayes progress purrr ranger Rdpack robustbase speedglm tester tidyr]; }; - Prostar = derive2 { name="Prostar"; version="1.32.1"; sha256="1gcmxzzzgj1kj3f6mnymh6k2g1q2qwm3vxi87z8iykiqbr3ri4fs"; depends=[DAPAR DAPARdata data_table future ggplot2 gplots highcharter htmlwidgets later promises rhandsontable shiny shinyAce shinyBS shinycssloaders shinyjqui shinyjs shinythemes tibble vioplot webshot]; }; + Prostar = derive2 { name="Prostar"; version="1.32.6"; sha256="0ydrpisl9b15m2fa0ba61glymd3xvq27pds4pk2zm3lazypm69gm"; depends=[Biobase 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="1.32.0"; sha256="0fgsb47qrvrl4y3yr094mas22rai5h5yl9mciadd6zcpamp2p01i"; depends=[]; }; ProteoDisco = derive2 { name="ProteoDisco"; version="1.6.0"; sha256="04m4lqiz43fscqbxjq3ymz8mhg88sihpchdv68pizsag7bz5bzjg"; depends=[BiocGenerics BiocParallel Biostrings checkmate cleaver dplyr GenomeInfoDb GenomicFeatures GenomicRanges IRanges ParallelLogger plyr rlang S4Vectors tibble tidyr VariantAnnotation XVector]; }; ProteoMM = derive2 { name="ProteoMM"; version="1.18.0"; sha256="1f2m3jdslp139bm0l40gcp5j27vjnp5a2zk8339zpp5j6ihhhvnw"; depends=[biomaRt gdata ggplot2 ggrepel gtools matrixStats]; }; @@ -794,7 +796,7 @@ in with self; { RCM = derive2 { name="RCM"; version="1.16.0"; sha256="0pqxhjqm2sfnifhqz8n6yc53npp32cpfdvhz5xk71f93mf3cdc13"; depends=[alabama DBI edgeR ggplot2 MASS nleqslv phyloseq RColorBrewer reshape2 tensor tseries VGAM]; }; RCSL = derive2 { name="RCSL"; version="1.8.0"; sha256="149bh9bd6h9qg82cnbnl9m8w8d10cw8b0z31qbyb9byfakn0a9hn"; depends=[ggplot2 igraph NbClust pracma RcppAnnoy Rtsne umap]; }; RCX = derive2 { name="RCX"; version="1.4.0"; sha256="1mpwb0j2zgbiqprn7gs9lcz4xpnnfllmgy2j2h9wkmac4241p1p9"; depends=[igraph jsonlite plyr]; }; - RCy3 = derive2 { name="RCy3"; version="2.20.0"; sha256="0n7k0v7inz2k6zap18sqqqa4d22px9lrxvp8anqh2vmgkkd789rc"; depends=[base64enc base64url BiocGenerics fs glue gplots graph httr IRdisplay IRkernel RColorBrewer RCurl RJSONIO uchardet uuid XML]; }; + RCy3 = derive2 { name="RCy3"; version="2.20.2"; sha256="1zy51ky7cqafw7j2z9gn68vacrlg4pa0kzsa1pi2jdiaisfyvmpf"; depends=[base64enc base64url BiocGenerics fs glue gplots graph httr IRdisplay IRkernel RColorBrewer RCurl RJSONIO uchardet uuid XML]; }; RCyjs = derive2 { name="RCyjs"; version="2.22.0"; sha256="0is771gp92m4hcvrajhrd8gi7akxrla9wwfal8pkcdac3gyv8z31"; depends=[base64enc BiocGenerics BrowserViz graph httpuv]; }; RDRToolbox = derive2 { name="RDRToolbox"; version="1.50.0"; sha256="1s7ab6mdarhsyhy1lsnf8kc60ba22gp2a4ydykwlwn0hx50zw6p5"; depends=[MASS rgl]; }; REBET = derive2 { name="REBET"; version="1.18.0"; sha256="0hhziwl6mhf8f63d2am2p1kkn15s9dd4vvlg70mzb0bw2mkfx83r"; depends=[ASSET]; }; @@ -844,11 +846,11 @@ in with self; { RUVnormalize = derive2 { name="RUVnormalize"; version="1.34.0"; sha256="0z8paxn57rnfg1mk96dnm9zrxahbd2203rwgwj3kzjnily6b09wp"; depends=[Biobase RUVnormalizeData]; }; RVS = derive2 { name="RVS"; version="1.22.0"; sha256="12219in1hcgrxb73m72cnsrd1723r85hyni2f2fhd595qw1bf3q8"; depends=[GENLIB gRain kinship2 snpStats]; }; RadioGx = derive2 { name="RadioGx"; version="2.4.0"; sha256="18zqfnwjil4mv7fgh4wvnniyybmyqkg0hk2wc57rcn0mlppa3602"; depends=[assertthat Biobase BiocGenerics BiocParallel caTools CoreGx data_table downloader magicaxis matrixStats RColorBrewer reshape2 S4Vectors scales SummarizedExperiment]; }; - RaggedExperiment = derive2 { name="RaggedExperiment"; version="1.24.0"; sha256="1xs7dz5mkh9zs078g2a0izij8vxrwhzh7gyjglp057gicsca0hal"; depends=[BiocGenerics GenomeInfoDb GenomicRanges IRanges Matrix MatrixGenerics S4Vectors SummarizedExperiment]; }; + RaggedExperiment = derive2 { name="RaggedExperiment"; version="1.24.2"; sha256="0aa886mmk1c5h1i3xnk4niq4ylrawpsn2f62hwmfj5dsyl8a36ka"; depends=[BiocGenerics GenomeInfoDb GenomicRanges IRanges Matrix MatrixGenerics S4Vectors SummarizedExperiment]; }; RandomWalkRestartMH = derive2 { name="RandomWalkRestartMH"; version="1.20.0"; sha256="0wm50c6677qycv30h1817babaxh97ggvbxhmk24y0dk63xkk4fh3"; depends=[dnet igraph Matrix]; }; RankProd = derive2 { name="RankProd"; version="3.26.0"; sha256="1nhhmwskj8ssapnfnj8hxmdbxknnzgcgbrdw2pzcyyjchqr7n9nf"; depends=[gmp Rmpfr]; }; RareVariantVis = derive2 { name="RareVariantVis"; version="2.28.0"; sha256="1q6bmmdc7jh1dacadww8pvhy1xd4wrk1v097irl34hw6p2pmd15d"; depends=[BiocGenerics BSgenome BSgenome_Hsapiens_UCSC_hg19 GenomeInfoDb GenomicFeatures GenomicRanges GenomicScores googleVis gtools IRanges phastCons100way_UCSC_hg19 S4Vectors SummarizedExperiment TxDb_Hsapiens_UCSC_hg19_knownGene VariantAnnotation]; }; - Rarr = derive2 { name="Rarr"; version="1.0.1"; sha256="1dn8sy8j5n9qwg7dxi87hrpvl78mslzlc7jxsfik3j20zyfkjcxq"; depends=[httr jsonlite paws_storage R_utils stringr]; }; + Rarr = derive2 { name="Rarr"; version="1.0.3"; sha256="0j8zc330qwzs40k90yg4adhs7prc2kyy2w4hn7rsq2vlcyxkgkam"; depends=[httr jsonlite paws_storage R_utils stringr]; }; RbcBook1 = derive2 { name="RbcBook1"; version="1.68.0"; sha256="0w0iccrwrvyrpr04kcdsqa7shdq4frn2kllx77947zrzszhwb1a4"; depends=[Biobase graph rpart]; }; Rbec = derive2 { name="Rbec"; version="1.8.0"; sha256="1acibbnkp3rv6mr4vi39ksc98fa0brcycxsq1zaz8mvd7vz3b6sq"; depends=[dada2 doParallel foreach ggplot2 Rcpp readr]; }; Rbowtie = derive2 { name="Rbowtie"; version="1.40.0"; sha256="1hfr1zdvikvygzgyy58f5rnz5jkmsrhwa930h331wx5012hhmnv7"; depends=[]; }; @@ -867,7 +869,7 @@ in with self; { ReactomeGraph4R = derive2 { name="ReactomeGraph4R"; version="1.8.0"; sha256="0bf6z1m5pdmaifa45bqkslkdsjvg7hsalj8aiqad831wd7s9x982"; depends=[data_table doParallel foreach getPass jsonlite magrittr neo4r purrr ReactomeContentService4R rlang]; }; ReactomePA = derive2 { name="ReactomePA"; version="1.44.0"; sha256="1hy8qz7d2826kf6pkl3v8cjwx35ap8xr92jw5wv445p3xcd1clzn"; depends=[AnnotationDbi DOSE enrichplot ggplot2 ggraph graphite gson igraph reactome_db]; }; ReadqPCR = derive2 { name="ReadqPCR"; version="1.46.0"; sha256="0i107z33vdhr69bwzmpfb8gqqfcv3aka87ws6dxg50xl2hx6ik3b"; depends=[Biobase]; }; - RedeR = derive2 { name="RedeR"; version="2.4.2"; sha256="02smz2v6py482cnj0rh35s3imqbd47iwjxvaab8sjp67l96df7h9"; depends=[igraph]; }; + RedeR = derive2 { name="RedeR"; version="2.4.3"; sha256="1fsdd4n4012m9ala3v7jpazb4vzlyj3y8ykygxk267n31dlwk1qm"; depends=[igraph]; }; RedisParam = derive2 { name="RedisParam"; version="1.2.0"; sha256="0y5pxh1fsksbhficl24zdi1kcjb88iw6yabj5adbkbx5da9mvymp"; depends=[BiocParallel futile_logger redux withr]; }; RefPlus = derive2 { name="RefPlus"; version="1.70.0"; sha256="0ii4pki0gqsfcjlfwq5hx67yf0id2krrgs8qnss4gijj27m8h86m"; depends=[affy affyPLM Biobase preprocessCore]; }; RegEnrich = derive2 { name="RegEnrich"; version="1.10.0"; sha256="09gkmna3w0x5m0mpq1llrqsrknlx2hncn74f4fksmx4r4mj0gphd"; depends=[BiocParallel BiocSet DESeq2 DOSE dplyr fgsea ggplot2 limma magrittr randomForest reshape2 S4Vectors SummarizedExperiment tibble WGCNA]; }; @@ -878,7 +880,7 @@ in with self; { Rfastp = derive2 { name="Rfastp"; version="1.10.0"; sha256="0c8nx0binn20vnxgsdpbc9lnjbc7j78f91ylgzwjw5ji4jfrzzhs"; depends=[ggplot2 Rcpp reshape2 Rhtslib rjson zlibbioc]; }; RgnTX = derive2 { name="RgnTX"; version="1.2.0"; sha256="150cyydkhp606l6a9h05h5lxir6jqxh40n7r9r4b3yiizlvnkvbp"; depends=[GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 IRanges regioneR S4Vectors TxDb_Hsapiens_UCSC_hg19_knownGene]; }; Rgraphviz = derive2 { name="Rgraphviz"; version="2.44.0"; sha256="1dv1vk73achjz5b5zzw2d517nbjfrlj7gppd48pfhk1w0mvz3q61"; depends=[graph]; }; - Rhdf5lib = derive2 { name="Rhdf5lib"; version="1.22.0"; sha256="1j8i4rmq85n7jys86a9zyj1n4qn7bhc1sqgcq8dyh7zqfdvb9bcw"; depends=[]; }; + Rhdf5lib = derive2 { name="Rhdf5lib"; version="1.22.1"; sha256="1007i2rzz86k04kswa4h53p8zzh52k31m9d8im6iw0n91inqbcj9"; depends=[]; }; Rhisat2 = derive2 { name="Rhisat2"; version="1.16.0"; sha256="1x9phnrk27v2r3ldqa9cd6yp2q3y5p2rm9wmra3wgrmhz9gxq1qy"; depends=[GenomicFeatures GenomicRanges SGSeq]; }; Rhtslib = derive2 { name="Rhtslib"; version="2.2.0"; sha256="1p8imns26knh21r254n7i9xvy8xzz3zizx0kq4si7cdaf2b4xayi"; depends=[zlibbioc]; }; RiboCrypt = derive2 { name="RiboCrypt"; version="1.6.0"; sha256="0dkdb5kmdgcg8l7l1dd1myx06sdvl7bvahqq1b5q7xz69vnslrfc"; depends=[BiocGenerics BiocParallel Biostrings bslib data_table dplyr GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 htmlwidgets httr IRanges jsonlite knitr markdown NGLVieweR ORFik plotly RCurl rlang shiny shinycssloaders shinyhelper shinyjqui stringr]; }; @@ -897,8 +899,8 @@ in with self; { Rsubread = derive2 { name="Rsubread"; version="2.14.2"; sha256="1dgbvhsd0rki1skwrb4acd3cfy7c9slsjq1s7r2469zbs3xf12xc"; depends=[Matrix]; }; Rtpca = derive2 { name="Rtpca"; version="1.10.0"; sha256="0wwrnkbzvdwayvw1x89jiknwsg95ijy0hik7lrp5k1qwm49w4dvl"; depends=[Biobase dplyr fdrtool ggplot2 pROC tibble tidyr]; }; Rtreemix = derive2 { name="Rtreemix"; version="1.62.0"; sha256="04glj66rf1jcy4qychjg5j2ssvk8g8zc15493a9l8b63m1ws06g3"; depends=[Biobase graph Hmisc]; }; - S4Arrays = derive2 { name="S4Arrays"; version="1.0.5"; sha256="01xlccybhdgas9pnx88ll9q56qb2xd687xvfrc7bd5r9sf72b81c"; depends=[abind BiocGenerics crayon IRanges Matrix S4Vectors]; }; - S4Vectors = derive2 { name="S4Vectors"; version="0.38.1"; sha256="0qpjx64ilc1niglhf6pn47damgaf5vdzwkvnlhcixqzpl28ndbs9"; depends=[BiocGenerics]; }; + S4Arrays = derive2 { name="S4Arrays"; version="1.0.6"; sha256="011n4lyznlrya5l8d7m30x81k7h81wbp07b12s6a4s5sy9fzd5jb"; depends=[abind BiocGenerics crayon IRanges Matrix S4Vectors]; }; + S4Vectors = derive2 { name="S4Vectors"; version="0.38.2"; sha256="0n1w451647pxii6qrrxbvdi9z6rqdwibczkbs7k7a9j33bv3nqv8"; depends=[BiocGenerics]; }; SAIGEgds = derive2 { name="SAIGEgds"; version="2.0.1"; sha256="0v1zfyvx3852kidh7hiyh1al86gs5v0dkx9laj8182pwsjy4qnys"; depends=[gdsfmt Matrix Rcpp RcppArmadillo RcppParallel SeqArray]; }; SANTA = derive2 { name="SANTA"; version="2.36.0"; sha256="0knc7lxlcjh9j144j7kirsknkk8qszmmjwg59v3050pi79m0czr9"; depends=[igraph Matrix]; }; SBGNview = derive2 { name="SBGNview"; version="1.14.0"; sha256="0krfmwdx2f849nsbhck5p2vgfrvqh0xb1pb4vx4rapdrvc1fpihg"; depends=[AnnotationDbi bookdown httr igraph KEGGREST knitr pathview Rdpack rmarkdown rsvg SBGNview_data SummarizedExperiment xml2]; }; @@ -907,7 +909,7 @@ in with self; { SCAN_UPC = derive2 { name="SCAN.UPC"; version="2.42.0"; sha256="1k9qzh1bk555ax1mm8w0r4rcvwaw5x1gyrzkamhgkh48m9abp6sq"; depends=[affy affyio Biobase Biostrings foreach GEOquery IRanges MASS oligo sva]; }; SCANVIS = derive2 { name="SCANVIS"; version="1.14.0"; sha256="07i481wk0v16r5bqjvmnys6cbd228hgzb6sp1975q595y5s76gnz"; depends=[IRanges plotrix RCurl rtracklayer]; }; SCATE = derive2 { name="SCATE"; version="1.10.0"; sha256="1fkswn9xlbr4mrnr62yzk51dri7rzbvf28whh7qhdfxgyvavw439"; depends=[GenomicAlignments GenomicRanges mclust preprocessCore Rtsne SCATEData splines2 xgboost]; }; - SCArray = derive2 { name="SCArray"; version="1.8.3"; sha256="0ww8bznlgb1806b7fj8zwhnrsqvyr7gwlsr5kyrvl7c27gjxivj0"; depends=[BiocParallel BiocSingular DelayedArray DelayedMatrixStats gdsfmt Matrix S4Vectors SingleCellExperiment SummarizedExperiment]; }; + SCArray = derive2 { name="SCArray"; version="1.8.4"; sha256="1svvq0ic6hlqi86lch3q5n4d71mxkq102x01nc3fgpf0bcv8rsaf"; depends=[BiocParallel BiocSingular DelayedArray DelayedMatrixStats gdsfmt Matrix S4Vectors SingleCellExperiment SummarizedExperiment]; }; SCArray_sat = derive2 { name="SCArray.sat"; version="1.0.3"; sha256="160x7wps2y4w8i0z97q8bgq0k8dih9axshha7wi6sx8j3qf6ab71"; depends=[BiocGenerics BiocParallel BiocSingular DelayedArray gdsfmt S4Vectors SCArray Seurat SeuratObject SummarizedExperiment]; }; SCBN = derive2 { name="SCBN"; version="1.18.0"; sha256="1b3hhj4lsafkrb86sr937vwjhymarxgx97bj3y51jg7jpqfi6gnr"; depends=[]; }; SCFA = derive2 { name="SCFA"; version="1.10.0"; sha256="1c9z8axz0vkcfq2il4qnqzjg9qklwsf4ijwb29kn711p96anfgw7"; depends=[BiocParallel cluster coro glmnet igraph Matrix matrixStats psych RhpcBLASctl survival torch]; }; @@ -937,7 +939,7 @@ in with self; { SOMNiBUS = derive2 { name="SOMNiBUS"; version="1.7.0"; sha256="19damf0rhq01gb7b1bjsivp28b57jq36zhry960yfahg09d13bqv"; depends=[Matrix mgcv VGAM]; }; SPEM = derive2 { name="SPEM"; version="1.40.0"; sha256="1475dl8dg1xiblvsk82infkhirmk9zjznrkvk1a3brlhs5cf1lq8"; depends=[Biobase Rsolnp]; }; SPIA = derive2 { name="SPIA"; version="2.52.0"; sha256="1f0d12y9al89c669y5c7byjgyml33jnn6s9iq1gcxm73ac6ws067"; depends=[KEGGgraph]; }; - SPIAT = derive2 { name="SPIAT"; version="1.2.2"; sha256="04vr7k8hb6x83w4my3ak6rj4c88nyyj0ma2yd74hs2c0392471cf"; depends=[apcluster dbscan dittoSeq dplyr ggplot2 gridExtra gtools mmand pracma RANN raster reshape2 sp SpatialExperiment spatstat_explore spatstat_geom SummarizedExperiment tibble vroom]; }; + SPIAT = derive2 { name="SPIAT"; version="1.2.3"; sha256="08qgy0lbh7zz0mcf7qfv9y570wwm4a2118adjmq9nraszc27wch3"; depends=[apcluster dbscan dittoSeq dplyr ggplot2 gridExtra gtools mmand pracma RANN raster reshape2 rlang sp SpatialExperiment spatstat_explore spatstat_geom SummarizedExperiment tibble vroom]; }; SPLINTER = derive2 { name="SPLINTER"; version="1.26.0"; sha256="1wh0msqbfnbygf1wjkryj8yx5f1c0w1hs5mmk8sky0sn0g32r7l4"; depends=[biomaRt Biostrings BSgenome_Mmusculus_UCSC_mm9 GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 googleVis Gviz IRanges plyr S4Vectors seqLogo stringr]; }; SPONGE = derive2 { name="SPONGE"; version="1.22.0"; sha256="1ayvigqj5j7s7031gpyhaz3m3z85w9j8j850pggshy9gixvy1mnp"; depends=[Biobase biomaRt caret ComplexHeatmap cvms data_table doRNG dplyr expm foreach ggplot2 ggpubr ggridges glmnet gRbase igraph iterators logging MASS MetBrewer miRBaseConverter ppcor randomForest rlang stringr tidyr tidyverse tnet]; }; SPOTlight = derive2 { name="SPOTlight"; version="1.4.1"; sha256="1z3mprlj6fvz90mra2gfaxgfi2k7mr98w0q11js47hqbymm436wx"; depends=[ggplot2 Matrix matrixStats NMF nnls SingleCellExperiment]; }; @@ -963,9 +965,10 @@ in with self; { SeqGate = derive2 { name="SeqGate"; version="1.10.0"; sha256="1v37dyz96zcgs0h44drkqw832zc90r37clk1yjhsm8m1ri59gdsh"; depends=[BiocManager GenomicRanges S4Vectors SummarizedExperiment]; }; SeqSQC = derive2 { name="SeqSQC"; version="1.22.0"; sha256="1s9qmvz8zhg90bz7dyp0cfk354plqx7kydjafbngg4vksbm1grg7"; depends=[e1071 ExperimentHub gdsfmt GenomicRanges GGally ggplot2 IRanges rbokeh RColorBrewer reshape2 rmarkdown S4Vectors SNPRelate]; }; SeqVarTools = derive2 { name="SeqVarTools"; version="1.38.0"; sha256="0qs67mdnw2kl45610nldsq40smy0hg5h8mndjvqvjynwkj9xjk0a"; depends=[Biobase BiocGenerics data_table gdsfmt GenomicRanges GWASExactHW IRanges logistf Matrix S4Vectors SeqArray]; }; + SharedObject = derive2 { name="SharedObject"; version="1.14.1"; sha256="0jlkkb6w237ym5jnn9i5j3swiq8x37fkq3flgf8g1svzxy9icvga"; depends=[BH BiocGenerics Rcpp]; }; ShortRead = derive2 { name="ShortRead"; version="1.58.0"; sha256="0wpr3ksr7j5yk6m1zaa47dwdgznajsz8as4p9vf7schaqvhq1wc4"; depends=[Biobase BiocGenerics BiocParallel Biostrings GenomeInfoDb GenomicAlignments GenomicRanges hwriter IRanges lattice latticeExtra Rhtslib Rsamtools S4Vectors XVector zlibbioc]; }; - SiPSiC = derive2 { name="SiPSiC"; version="1.0.0"; sha256="11h7yn5sqispclsbxgchdraf5a35sq544sg0brp9nqhhwxjgl86r"; depends=[Matrix SingleCellExperiment]; }; - SigCheck = derive2 { name="SigCheck"; version="2.32.0"; sha256="0g407p7b4q3sp0i7wvhyxyah17jhv4gy9ssipk099y7k6chii1rl"; depends=[Biobase BiocParallel e1071 MLInterfaces survival]; }; + SiPSiC = derive2 { name="SiPSiC"; version="1.0.2"; sha256="1q79vbfj65ndyb9qb0bdk5zzasvg991p4069akvn07z863fhwnrs"; depends=[Matrix SingleCellExperiment]; }; + SigCheck = derive2 { name="SigCheck"; version="2.32.1"; sha256="0lv75kj0h84ri0advwr6sm2mdsgpd7pkql34nsmar11xxks5bwbf"; depends=[Biobase BiocParallel e1071 MLInterfaces survival]; }; SigFuge = derive2 { name="SigFuge"; version="1.38.0"; sha256="1nn124y33bvw77ylz9dykrd43089ajghmd74f7wzhn6sfmjisd2f"; depends=[GenomicRanges ggplot2 matlab reshape sigclust]; }; SigsPack = derive2 { name="SigsPack"; version="1.14.0"; sha256="03sqv0jp9539qmjb81avi8l93r25r5gsqfwzqgfpdg8d5anh7lp3"; depends=[Biobase Biostrings BSgenome GenomeInfoDb GenomicRanges quadprog rtracklayer SummarizedExperiment VariantAnnotation]; }; SimBindProfiles = derive2 { name="SimBindProfiles"; version="1.38.0"; sha256="0z53dyrkbawbj8f01gf58cljz7vsvc9dd3jfhvvc2mfxfm0bfrl1"; depends=[Biobase limma mclust Ringo]; }; @@ -978,15 +981,15 @@ in with self; { SomaticSignatures = derive2 { name="SomaticSignatures"; version="2.36.0"; sha256="075w88x7lv2fkp2ipqgxp4pzh6kbjw3nmp0qra2p4fss4j3g8d6s"; depends=[Biobase Biostrings GenomeInfoDb GenomicRanges ggbio ggplot2 IRanges NMF pcaMethods proxy reshape2 S4Vectors VariantAnnotation]; }; SpacePAC = derive2 { name="SpacePAC"; version="1.38.0"; sha256="0l6drsrxk2fxhq5dk0186z6mbc7hvyng4116y5fc8j9kxjc0rfna"; depends=[iPAC]; }; Spaniel = derive2 { name="Spaniel"; version="1.14.0"; sha256="17b8gfyalb0hfrpv4islkvjg8d06nff79zkyl261bg51dydv2cfw"; depends=[dplyr DropletUtils ggplot2 igraph jpeg jsonlite magrittr png S4Vectors scater scran Seurat shiny SingleCellExperiment SummarizedExperiment]; }; - SparseArray = derive2 { name="SparseArray"; version="1.0.11"; sha256="1vx7kwv9rw1b9r04wv0bsqjwpb3jg9j9z4smq4a5cr1k2ndh2n35"; depends=[BiocGenerics IRanges Matrix MatrixGenerics matrixStats S4Arrays S4Vectors XVector]; }; + SparseArray = derive2 { name="SparseArray"; version="1.0.12"; sha256="1rgxr087paqxv8q5say8zvhqm4znav6vb6ic5jyskq8bxm7ih10f"; depends=[BiocGenerics IRanges Matrix MatrixGenerics matrixStats S4Arrays S4Vectors XVector]; }; SparseSignatures = derive2 { name="SparseSignatures"; version="2.10.0"; sha256="0bqwhhcsj72a4ci0j6k5bc4rm6q8vlhmhp1h3il73imj7lkdll6z"; depends=[Biostrings BSgenome data_table GenomeInfoDb GenomicRanges ggplot2 gridExtra IRanges NMF nnlasso nnls reshape2]; }; SpatialCPie = derive2 { name="SpatialCPie"; version="1.16.0"; sha256="1qli4hcpjxq5q1c6j08sc251d39phzrgc999zq1splzsnkbprq9s"; depends=[colorspace data_table digest dplyr ggforce ggiraph ggplot2 ggrepel igraph lpSolve purrr readr rlang shiny shinycssloaders shinyjs shinyWidgets SummarizedExperiment tibble tidyr tidyselect zeallot]; }; SpatialDecon = derive2 { name="SpatialDecon"; version="1.10.0"; sha256="0x3m60a93l4sg4nggnsdysxqaji8wy6rvncvhq4z67zzax5sj8ia"; depends=[Biobase GeomxTools logNormReg Matrix repmis SeuratObject]; }; SpatialExperiment = derive2 { name="SpatialExperiment"; version="1.10.0"; sha256="18fcfyjvp9nzadlicsnz62wva8ik0z6jqg1b906avm2vk6rbxw70"; depends=[BiocFileCache BiocGenerics DropletUtils magick rjson S4Vectors SingleCellExperiment SummarizedExperiment]; }; - SpatialFeatureExperiment = derive2 { name="SpatialFeatureExperiment"; version="1.2.2"; sha256="1zmsjzxn2k5v5j6m9pxd9665wqk4kkpxvwm029z7khwb7l6xdl0p"; depends=[BiocGenerics BiocNeighbors BiocParallel Matrix rjson rlang S4Vectors sf SingleCellExperiment SpatialExperiment spdep SummarizedExperiment terra]; }; + SpatialFeatureExperiment = derive2 { name="SpatialFeatureExperiment"; version="1.2.3"; sha256="1w8m05iqdw0b2xfsn5sjccj2h4kx14zxv44gw2f1sy77sslzpmy0"; depends=[BiocGenerics BiocNeighbors BiocParallel Matrix rjson rlang S4Vectors sf SingleCellExperiment SpatialExperiment spdep SummarizedExperiment terra]; }; SpatialOmicsOverlay = derive2 { name="SpatialOmicsOverlay"; version="1.0.0"; sha256="10w8caqjiqsrjxzkxa8a3ngzar2kbax73rcyjgb6f2kwjmxxij3i"; depends=[base64enc Biobase BiocFileCache data_table dplyr EBImage GeomxTools ggplot2 ggtext magick pbapply plotrix RBioFormats readxl S4Vectors scattermore stringr XML]; }; SpeCond = derive2 { name="SpeCond"; version="1.54.0"; sha256="164hks3bz5yszhq3dkdaxwggp4pdyg5k1yypkagd6myd5h5hg5nn"; depends=[Biobase fields hwriter mclust RColorBrewer]; }; - Spectra = derive2 { name="Spectra"; version="1.10.2"; sha256="1jrlfm6k6v4vhzl4lg6sa49yw35ds9x3v7iyc2cvbxqmpp5haila"; depends=[BiocGenerics BiocParallel fs IRanges MsCoreUtils ProtGenerics S4Vectors]; }; + Spectra = derive2 { name="Spectra"; version="1.10.3"; sha256="1fx6xkl29frfk8bzz5jvr1cn0hjyi46ck23izb1cypiag4lsrf8v"; depends=[BiocGenerics BiocParallel fs IRanges MsCoreUtils ProtGenerics S4Vectors]; }; SpectralTAD = derive2 { name="SpectralTAD"; version="1.16.1"; sha256="0l49fwr038ic2k87fxcjwdlwjd49wyywxjsa2d6ffncwmgaqrpc2"; depends=[BiocParallel cluster dplyr GenomicRanges HiCcompare magrittr Matrix PRIMME]; }; SpidermiR = derive2 { name="SpidermiR"; version="1.30.0"; sha256="00p98wvj56v70gdc14wbbjgcvmpxn8ckb4zh8lbjdiplsn815g31"; depends=[AnnotationDbi gdata httr igraph miRNAtap miRNAtap_db org_Hs_eg_db]; }; SpliceWiz = derive2 { name="SpliceWiz"; version="1.2.3"; sha256="10sg5hfcfrcgk73ymmqpx0xx2slfcdwaxj70yq4312dijy3gk9x7"; depends=[AnnotationHub BiocFileCache BiocGenerics BiocParallel Biostrings BSgenome data_table DelayedArray DelayedMatrixStats DT fst genefilter GenomeInfoDb GenomicRanges ggplot2 HDF5Array heatmaply htmltools IRanges magrittr matrixStats NxtIRFdata ompBAM patchwork pheatmap plotly progress R_utils RColorBrewer Rcpp RcppProgress rhandsontable rhdf5 rtracklayer rvest S4Vectors scales shiny shinydashboard shinyFiles shinyWidgets stringi SummarizedExperiment zlibbioc]; }; @@ -994,7 +997,7 @@ in with self; { SplicingGraphs = derive2 { name="SplicingGraphs"; version="1.40.0"; sha256="0lcx7q5anv04flv4fjaqz0rw0xazx5q25xjq4fq2zm0syyxa5p2z"; depends=[BiocGenerics BiocParallel GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges graph igraph IRanges Rgraphviz Rsamtools S4Vectors]; }; SpotClean = derive2 { name="SpotClean"; version="1.2.0"; sha256="1q81xmn56b8cvlnn7kzjm3qlys771z9z260mdcininn8sizirmqq"; depends=[dplyr ggplot2 Matrix RColorBrewer readbitmap rhdf5 rjson rlang S4Vectors Seurat SpatialExperiment SummarizedExperiment tibble viridis]; }; StarBioTrek = derive2 { name="StarBioTrek"; version="1.26.0"; sha256="0x1x582favjv8f14milkv8cg8f4m3af0i4mscf7gfgdngy6w9wph"; depends=[AnnotationDbi e1071 ggplot2 graphite igraph MLmetrics reshape2 ROCR SpidermiR]; }; - Statial = derive2 { name="Statial"; version="1.2.2"; sha256="0nhwxd0rsri3lsbk7mziw5z77624rlq0nikkrb1iba4y1cpx3fgz"; depends=[BiocParallel concaveman data_table dplyr ggplot2 limma magrittr plotly purrr ranger S4Vectors SingleCellExperiment SpatialExperiment spatstat_explore spatstat_geom stringr SummarizedExperiment tibble tidyr tidyselect]; }; + Statial = derive2 { name="Statial"; version="1.2.4"; sha256="1rpq0yq5lb5ca0v8xgspnkyha8xlpx1sikmj4d3fj0r57fb6zr93"; depends=[BiocParallel concaveman data_table dplyr ggplot2 limma magrittr plotly purrr ranger S4Vectors SingleCellExperiment SpatialExperiment spatstat_explore spatstat_geom stringr SummarizedExperiment tibble tidyr tidyselect]; }; Streamer = derive2 { name="Streamer"; version="1.46.0"; sha256="13ww5akkmakmr9r693pv5j36mvqwrbk0vha98sm8laf4qr5my3iq"; depends=[BiocGenerics graph RBGL]; }; Structstrings = derive2 { name="Structstrings"; version="1.16.0"; sha256="0aylyb3063cas3nbr8n5w4sq897mw9i5wfk404f4n6w5zsi0xrj9"; depends=[BiocGenerics Biostrings crayon IRanges S4Vectors stringi stringr XVector]; }; StructuralVariantAnnotation = derive2 { name="StructuralVariantAnnotation"; version="1.16.0"; sha256="0gkps2pls9bpqr8sxm8zwdkn156g8r6mhf4bx17nif5s35qld1rb"; depends=[assertthat BiocGenerics Biostrings dplyr GenomeInfoDb GenomicFeatures GenomicRanges IRanges rlang rtracklayer S4Vectors stringr SummarizedExperiment VariantAnnotation]; }; @@ -1008,9 +1011,9 @@ in with self; { TADCompare = derive2 { name="TADCompare"; version="1.10.0"; sha256="1sykkvq20490q66lzafbl76167srcjl1zmphd4b0wszwhg2xnxx9"; depends=[cluster cowplot dplyr ggplot2 ggpubr HiCcompare magrittr Matrix PRIMME RColorBrewer reshape2 tidyr]; }; TAPseq = derive2 { name="TAPseq"; version="1.12.0"; sha256="1fgqz21fvfxaqhrvlqynsv0inkxzvjp8kac7pr0gb84p3xwg75y4"; depends=[BiocGenerics BiocParallel Biostrings BSgenome dplyr GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges S4Vectors tidyr]; }; TBSignatureProfiler = derive2 { name="TBSignatureProfiler"; version="1.12.0"; sha256="1skakx7dy0jd180yww49swvg95irxxsfh9p58pq521hx7nwlcki2"; depends=[ASSIGN BiocParallel ComplexHeatmap DESeq2 DT edgeR gdata ggplot2 GSVA magrittr RColorBrewer reshape2 rlang ROCit S4Vectors singscore SummarizedExperiment]; }; - TCGAbiolinks = derive2 { name="TCGAbiolinks"; version="2.28.3"; sha256="1hh09ya4jg062k1ibp1cpvdrgv6gwr95ch57iycgd3cjc5g0xhii"; depends=[biomaRt data_table downloader dplyr GenomicRanges ggplot2 httr IRanges jsonlite knitr plyr purrr R_utils readr rvest S4Vectors stringr SummarizedExperiment TCGAbiolinksGUI_data tibble tidyr XML xml2]; }; - TCGAutils = derive2 { name="TCGAutils"; version="1.20.2"; sha256="0nnfrd5x3mii9adizvz79jinlxn2lhg4civ9v0wwygmdhk7rrm1n"; depends=[AnnotationDbi BiocGenerics GenomeInfoDb GenomicDataCommons GenomicFeatures GenomicRanges IRanges MultiAssayExperiment RaggedExperiment rvest S4Vectors stringr SummarizedExperiment xml2]; }; - TCseq = derive2 { name="TCseq"; version="1.23.0"; sha256="0fdz5qcp6axqgai64g6nf1ci27k1g3wlw3sczf5x5ki91jpan5vi"; depends=[BiocGenerics cluster e1071 edgeR GenomicAlignments GenomicRanges ggplot2 IRanges locfit reshape2 Rsamtools SummarizedExperiment]; }; + TCGAbiolinks = derive2 { name="TCGAbiolinks"; version="2.28.4"; sha256="1q7d3c37nwyr0hl21v2bzkvnzksq16vkbisnm1p9ldg90qkvdbzk"; depends=[biomaRt data_table downloader dplyr GenomicRanges ggplot2 httr IRanges jsonlite knitr plyr purrr R_utils readr rvest S4Vectors stringr SummarizedExperiment TCGAbiolinksGUI_data tibble tidyr XML xml2]; }; + TCGAutils = derive2 { name="TCGAutils"; version="1.20.4"; sha256="02mkijvh2h58wg7hsi76ycw6gapl0ai190agckaw4l54sqpsx91q"; depends=[AnnotationDbi BiocBaseUtils BiocGenerics GenomeInfoDb GenomicDataCommons GenomicFeatures GenomicRanges IRanges MultiAssayExperiment RaggedExperiment rvest S4Vectors stringr SummarizedExperiment xml2]; }; + TCseq = derive2 { name="TCseq"; version="1.24.3"; sha256="1l8ghap0yq07p8qj7z3d0a4rb2q913xi2my5bsjbl67hm6wpjm87"; depends=[BiocGenerics cluster e1071 edgeR GenomicAlignments GenomicRanges ggplot2 IRanges locfit reshape2 Rsamtools SummarizedExperiment]; }; TDbasedUFE = derive2 { name="TDbasedUFE"; version="1.0.0"; sha256="1hsjqcrp9fcn28aqvvrd51x75cyh1awzcqdqaxdxg0x2gn548jmf"; depends=[GenomicRanges MOFAdata readr rTensor shiny tximport tximportData]; }; TDbasedUFEadv = derive2 { name="TDbasedUFEadv"; version="1.0.0"; sha256="1i38wr1imzddsxby43jg5ag3dbprpzkcqa6s7b49a6xn88qrsxrq"; depends=[Biobase DOSE enrichplot enrichR GenomicRanges hash RTCGA rTensor shiny STRINGdb TDbasedUFE]; }; TEKRABber = derive2 { name="TEKRABber"; version="1.4.0"; sha256="01jk7iax89p5m3pqpjmbbiza1ij768wzm5b9vss9j7vyc2hrym3c"; depends=[apeglm biomaRt DESeq2 dplyr magrittr Rcpp SCBN SummarizedExperiment]; }; @@ -1071,7 +1074,7 @@ in with self; { VegaMC = derive2 { name="VegaMC"; version="3.38.0"; sha256="0vz8jj1vaghbs6i2m4ik2lkhjn3vz8qla8i8kgmbc4wj5ny32q9k"; depends=[Biobase biomaRt]; }; VennDetail = derive2 { name="VennDetail"; version="1.16.0"; sha256="126a0zpn6vw5l65zlcd8m53gfs4fdgj1nzw1fv0bqk8jiv44q87b"; depends=[dplyr futile_logger ggplot2 magrittr purrr tibble UpSetR VennDiagram]; }; ViSEAGO = derive2 { name="ViSEAGO"; version="1.14.0"; sha256="1d8473i0hk4d6kncvrv7xrsbayjkwnpln22d7xrll9kmhvkr679b"; depends=[AnnotationDbi AnnotationForge biomaRt data_table dendextend DiagrammeR DT dynamicTreeCut fgsea ggplot2 GO_db GOSemSim heatmaply htmlwidgets igraph plotly processx R_utils RColorBrewer scales topGO UpSetR]; }; - Voyager = derive2 { name="Voyager"; version="1.2.4"; sha256="0prl25qjl1s6qpxqcg99g890s8w233z02phidm24hap6yvcdvsz5"; depends=[BiocParallel bluster ggnewscale ggplot2 lifecycle Matrix patchwork rlang RSpectra S4Vectors scales scico sf SingleCellExperiment sparseMatrixStats SpatialExperiment SpatialFeatureExperiment spdep SummarizedExperiment terra]; }; + Voyager = derive2 { name="Voyager"; version="1.2.7"; sha256="0rvszinn1jvb85qw4mfcz5pw20354azz6bmmcfidrh60likc3p5q"; depends=[BiocParallel bluster ggnewscale ggplot2 lifecycle Matrix matrixStats patchwork rlang RSpectra S4Vectors scales scico sf SingleCellExperiment SpatialExperiment SpatialFeatureExperiment spdep SummarizedExperiment terra]; }; VplotR = derive2 { name="VplotR"; version="1.10.0"; sha256="02b82ajbq2448b9h6jx24jsrxavgm6bfn6kk1v2xf2fcipdx8chs"; depends=[cowplot GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 IRanges magrittr RColorBrewer reshape2 Rsamtools S4Vectors zoo]; }; Wrench = derive2 { name="Wrench"; version="1.18.0"; sha256="18x12395928d0mf8kffmdjqkdxrzgqzzhhvs7sdzldwyas6hfg2h"; depends=[limma locfit matrixStats]; }; XDE = derive2 { name="XDE"; version="2.46.0"; sha256="096pbkj4sw9kx2k25yw78zb2y615w86cvrgjk1xkvyi0w6v8mk6m"; depends=[Biobase BiocGenerics genefilter GeneMeta gtools mvtnorm RColorBrewer siggenes]; }; @@ -1079,7 +1082,7 @@ in with self; { XNAString = derive2 { name="XNAString"; version="1.8.0"; sha256="0xq39n1y807vv14fx57w6iz3kln384c6igmdphi1cli7b228xyh5"; depends=[Biostrings BSgenome data_table formattable future_apply GenomicRanges IRanges Rcpp S4Vectors stringi stringr]; }; XVector = derive2 { name="XVector"; version="0.40.0"; sha256="1v10hfz658gnb6p7pzdl28jbyypv91wx70i0dvi384nfgznhvmj2"; depends=[BiocGenerics IRanges S4Vectors zlibbioc]; }; Xeva = derive2 { name="Xeva"; version="1.16.0"; sha256="0q1y9qlfr7qbgdmxfrwizx94qp5ddsmkq295lh87qhjx8vv90fcs"; depends=[BBmisc Biobase ComplexHeatmap doParallel downloader ggplot2 nlme PharmacoGx Rmisc scales]; }; - YAPSA = derive2 { name="YAPSA"; version="1.25.0"; sha256="0xva7vljq2k78rzjnjlp4x3ylwk86jaqn2cgbff4h4sb8rfdya7c"; depends=[Biostrings BSgenome_Hsapiens_UCSC_hg19 circlize ComplexHeatmap corrplot dendextend doParallel dplyr GenomeInfoDb GenomicRanges GetoptLong ggbeeswarm ggplot2 gridExtra gtrellis KEGGREST limSolve magrittr PMCMRplus pracma reshape2 SomaticSignatures VariantAnnotation]; }; + YAPSA = derive2 { name="YAPSA"; version="1.26.8"; sha256="16rr2bkni3jx5qskr5fz5lvf23d03xgd3m4068mnd3n9r23hpb4p"; depends=[Biostrings BSgenome_Hsapiens_UCSC_hg19 circlize ComplexHeatmap corrplot dendextend doParallel dplyr GenomeInfoDb GenomicRanges GetoptLong ggbeeswarm ggplot2 gridExtra gtrellis KEGGREST limSolve magrittr PMCMRplus pracma reshape2 SomaticSignatures VariantAnnotation]; }; ZygosityPredictor = derive2 { name="ZygosityPredictor"; version="1.0.3"; sha256="0sbb2s851fx52rds4mj8qppd1pv5i333z00snypb8illvlid7mk3"; depends=[DelayedArray dplyr GenomicAlignments GenomicRanges igraph IRanges purrr Rsamtools stringr tibble VariantAnnotation]; }; a4 = derive2 { name="a4"; version="1.48.0"; sha256="0n49scwwmg51gcakbc0bfjcy1lcpdxg974l11yk35kj0bg9ynpgi"; depends=[a4Base a4Classif a4Core a4Preproc a4Reporting]; }; a4Base = derive2 { name="a4Base"; version="1.48.0"; sha256="01c8rps321820b0pchfqv8shglb26rys7hqkwygpzzx3jj310v8x"; depends=[a4Core a4Preproc annaffy Biobase genefilter glmnet gplots limma mpm multtest]; }; @@ -1144,7 +1147,7 @@ in with self; { awst = derive2 { name="awst"; version="1.8.0"; sha256="0nwpfxfrx9rw4vl02vr311ivmmk96ajlwyhwms642hjv74j2yiji"; depends=[SummarizedExperiment]; }; bacon = derive2 { name="bacon"; version="1.28.0"; sha256="1h2yh85c6d4j2abdh5l7m6zcxh9i5xzrwwjkwas4nfs48h74z293"; depends=[BiocParallel ellipse ggplot2]; }; ballgown = derive2 { name="ballgown"; version="2.32.0"; sha256="05lvpvy4gs3vg4ks23prx0mdp730h1m9kpg4al03ah062gyq3ahx"; depends=[Biobase GenomeInfoDb GenomicRanges IRanges limma RColorBrewer rtracklayer S4Vectors sva]; }; - bambu = derive2 { name="bambu"; version="3.2.5"; sha256="1vqxmz2lknnx1g61y7skvznsnxv3clajngz9mnggg1z3p5mr6cnh"; depends=[BiocGenerics BiocParallel BSgenome data_table dplyr GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges Rcpp RcppArmadillo Rsamtools S4Vectors SummarizedExperiment tidyr xgboost]; }; + bambu = derive2 { name="bambu"; version="3.2.6"; sha256="0h7ps32vbcn4hjpfb343nn8b50zq9my0k61847fi69vc4siwcx5k"; depends=[BiocGenerics BiocParallel BSgenome data_table dplyr GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges Rcpp RcppArmadillo Rsamtools S4Vectors SummarizedExperiment tidyr xgboost]; }; bamsignals = derive2 { name="bamsignals"; version="1.32.0"; sha256="18058j3fc47qcwvzgpb8mbc7cd1pywzrz3a36iqz93ihzjmymydk"; depends=[BiocGenerics GenomicRanges IRanges Rcpp Rhtslib zlibbioc]; }; bandle = derive2 { name="bandle"; version="1.4.1"; sha256="0zsrj6jbmyrsw0i69f38rr56qywcp4yy9b2zkhmbm1g1byy5rm3b"; depends=[BH Biobase BiocParallel BiocStyle circlize dplyr ggalluvial ggplot2 ggrepel knitr lbfgs MSnbase plyr pRoloc pRolocdata Rcpp RcppArmadillo rlang robustbase S4Vectors tidyr]; }; banocc = derive2 { name="banocc"; version="1.24.0"; sha256="0yi70y87isb34jc1wrnz4gr0d0f2zw44555s50j3qdnj1x8cld9y"; depends=[coda mvtnorm rstan stringr]; }; @@ -1169,12 +1172,12 @@ in with self; { biobroom = derive2 { name="biobroom"; version="1.32.0"; sha256="0kb6ylq94vywfky0mcrva109darcv361sqvwb19qn92p8vh5199l"; depends=[Biobase broom dplyr tidyr]; }; biobtreeR = derive2 { name="biobtreeR"; version="1.12.0"; sha256="0cbhlxh0w736695niyjd59fcvplna2f2x2av9k0sd1r3dy6lrcd4"; depends=[httpuv httr jsonlite stringi]; }; biocGraph = derive2 { name="biocGraph"; version="1.62.0"; sha256="0fnncmi82qb9lkg1zfyps7n3nrw1s3wcqbixh420w53hmdyryryl"; depends=[BiocGenerics geneplotter graph Rgraphviz]; }; - biocViews = derive2 { name="biocViews"; version="1.68.1"; sha256="04rzrwxd9n4l3agmbkx03hhcmy2fx049q5n4glld46mvx3vjvc48"; depends=[Biobase BiocManager graph RBGL RCurl RUnit XML]; }; + biocViews = derive2 { name="biocViews"; version="1.68.2"; sha256="1icnaj1ifndym7nl1yafzd0y0fxyhzjyb4qzqpcnsqhh4yi3pnm5"; depends=[Biobase BiocManager graph RBGL RCurl RUnit XML]; }; biocthis = derive2 { name="biocthis"; version="1.10.3"; sha256="1v0qrypdzl1bg85k8i7qamb6709cgk4ypmisjh6bn5r36nqd5qx4"; depends=[BiocManager fs glue rlang styler usethis]; }; - biodb = derive2 { name="biodb"; version="1.8.0"; sha256="1lcjq1zfarhc7pqqrkqnaycsv2f27n4n8mfvrc3c9ww4lsza555k"; depends=[BiocFileCache chk jsonlite lgr lifecycle openssl plyr progress R6 rappdirs Rcpp RCurl RSQLite stringr testthat withr XML yaml]; }; + biodb = derive2 { name="biodb"; version="1.8.1"; sha256="18j70ma85qb42qqpzz8fw3g4x6cav4j0pc2ab5ym22791dr8izck"; depends=[BiocFileCache chk git2r jsonlite lgr lifecycle openssl plyr progress R6 rappdirs Rcpp RCurl RSQLite stringr testthat withr XML yaml]; }; biodbChebi = derive2 { name="biodbChebi"; version="1.6.0"; sha256="1c4955rj8g03kjdr8x4296vz8spj957b65dmy8dw2f56ph1wc6aj"; depends=[biodb R6]; }; biodbExpasy = derive2 { name="biodbExpasy"; version="1.4.0"; sha256="0gwfs6b3ppas26k555pj9yjs949a7zxznbnkr0hn0x927z2lq60r"; depends=[biodb chk R6 stringr]; }; - biodbHmdb = derive2 { name="biodbHmdb"; version="1.6.0"; sha256="0qh8jvkk8n6hxjxwyp351s6v1dl6q5vxlx2ihg6hkswdavx8cgl8"; depends=[biodb R6 Rcpp testthat]; }; + biodbHmdb = derive2 { name="biodbHmdb"; version="1.6.1"; sha256="173wpnxdq3146ynr913wb0zscg2ga2w3jjv23v044vcjamwhh15p"; depends=[biodb R6 Rcpp testthat zip]; }; biodbKegg = derive2 { name="biodbKegg"; version="1.6.1"; sha256="0dnl26cvqy0v61aj1ddcbkqiz254n8vsrpy1hmkn7d1jrlkqsp4w"; depends=[biodb chk lifecycle R6]; }; biodbLipidmaps = derive2 { name="biodbLipidmaps"; version="1.6.0"; sha256="1j3ywrg1hilgx2d8a81y46s6x2yb03014i3dma5fjf5r9fhans03"; depends=[biodb lifecycle R6]; }; biodbMirbase = derive2 { name="biodbMirbase"; version="1.4.0"; sha256="09w4pckjg26333z6j27f1pw1bkxw4793fyk8q04b8ww1fnd7znr2"; depends=[biodb chk R6 stringr]; }; @@ -1198,11 +1201,11 @@ in with self; { breakpointR = derive2 { name="breakpointR"; version="1.18.0"; sha256="001n99lilymgqxmpi4v89gw60j1mx13rvppv1ff1pbnk1zcmg53n"; depends=[BiocGenerics breakpointRdata cowplot doParallel foreach GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 gtools IRanges Rsamtools S4Vectors]; }; brendaDb = derive2 { name="brendaDb"; version="1.14.0"; sha256="1kvb87cg9f3h7hnvxc2zgr9sxxcn0k09gmhp63g7szkqb41vkjyj"; depends=[BiocFileCache BiocParallel crayon dplyr magrittr purrr rappdirs Rcpp rlang stringr tibble tidyr]; }; bsseq = derive2 { name="bsseq"; version="1.36.0"; sha256="1mvhh99h1l6f5rlz0fzqkjpz9hblj2rbv8nx4j9n93g8riz7wsi3"; depends=[beachmat Biobase BiocGenerics BiocParallel Biostrings BSgenome data_table DelayedArray DelayedMatrixStats GenomeInfoDb GenomicRanges gtools HDF5Array IRanges limma locfit permute R_utils Rcpp rhdf5 S4Vectors scales SummarizedExperiment]; }; - bugsigdbr = derive2 { name="bugsigdbr"; version="1.6.4"; sha256="1mw895mspfl05pfm5h4r3fyh8hnzklx30k44v7xg67dc83pdrlk6"; depends=[BiocFileCache vroom]; }; + bugsigdbr = derive2 { name="bugsigdbr"; version="1.6.6"; sha256="14cn1yj44y39v0bq6db282lw0vj1janlmwkz2yxngg8lsz1m9w6n"; depends=[BiocFileCache vroom]; }; bumphunter = derive2 { name="bumphunter"; version="1.42.0"; sha256="1xghz87702fg9r6n1igygf4ybb8mw8ff0i02qkx9jmm6vmmfhv18"; depends=[AnnotationDbi BiocGenerics doRNG foreach GenomeInfoDb GenomicFeatures GenomicRanges IRanges iterators limma locfit matrixStats S4Vectors]; }; cBioPortalData = derive2 { name="cBioPortalData"; version="2.12.0"; sha256="0dhxjj63ddyjvh2s327336w6711c1a53kw7xiwwaxxmzqncrqik6"; depends=[AnVIL BiocFileCache digest dplyr GenomeInfoDb GenomicRanges httr IRanges MultiAssayExperiment RaggedExperiment readr RTCGAToolbox S4Vectors SummarizedExperiment TCGAutils tibble tidyr]; }; cTRAP = derive2 { name="cTRAP"; version="1.18.0"; sha256="0qbzxkjw0l37b0xs2k54va236k56hl652j77yp06d2r451gl3k8h"; depends=[AnnotationDbi AnnotationHub binr cowplot data_table dplyr DT fastmatch fgsea ggplot2 ggrepel highcharter htmltools httr limma pbapply purrr qs R_utils readxl reshape2 rhdf5 rlang scales shiny shinycssloaders tibble]; }; - cageminer = derive2 { name="cageminer"; version="1.6.1"; sha256="0nw21zbh83zz59zcp01s86xzfzynf91hjxzrjncb7jp6hsq6g13c"; depends=[BioNERO GenomeInfoDb GenomicRanges ggbio ggplot2 ggtext IRanges reshape2 rlang]; }; + cageminer = derive2 { name="cageminer"; version="1.6.2"; sha256="1pmmgv8shjrrrddbgyfsjfip6wfr6i06xpwf7j8wp7azmgf8vrh5"; depends=[BioNERO GenomeInfoDb GenomicRanges ggbio ggplot2 ggtext IRanges reshape2 rlang]; }; calm = derive2 { name="calm"; version="1.14.0"; sha256="07wnfspw81my0lsbpdxn8qh9flsm28b9w748cswbs42c7gffgjbp"; depends=[mgcv]; }; canceR = derive2 { name="canceR"; version="1.34.0"; sha256="0agmw839frjz7zf1px7l8b0xk05gj2isgfvl88dwgxkww68vrpbb"; depends=[Biobase circlize Formula geNetClassifier GSEABase httr phenoTest plyr R_methodsS3 R_oo rpart RUnit survival tkrplot]; }; cancerclass = derive2 { name="cancerclass"; version="1.44.0"; sha256="0bwrzqhfk6vma1pybmn7bs4asr8r2n3g8l2mmw93rqjb8p319shd"; depends=[binom Biobase]; }; @@ -1223,7 +1226,7 @@ in with self; { cellity = derive2 { name="cellity"; version="1.28.0"; sha256="1n9i3vkc01fdv5fxwqnw2zd42wmn3n80ryidzzq874i77nid9mgl"; depends=[AnnotationDbi e1071 ggplot2 mvoutlier org_Hs_eg_db org_Mm_eg_db robustbase topGO]; }; cellmigRation = derive2 { name="cellmigRation"; version="1.8.0"; sha256="1d1js0pvqlc59wpl9mdj0fjw2gx0bjs2p7v2si6rv6j03zz916ka"; depends=[doParallel FactoMineR FME foreach Hmisc matrixStats reshape2 sp SpatialTools tiff vioplot]; }; cellscape = derive2 { name="cellscape"; version="1.24.0"; sha256="0g7way8s7xmdx8266vv4597znyh4kkmc1cvxg4i0x3wkv2rq4gac"; depends=[dplyr gtools htmlwidgets jsonlite plyr reshape2 stringr]; }; - cellxgenedp = derive2 { name="cellxgenedp"; version="1.4.0"; sha256="0frbajznfdvbjxyqb807wb80i0gi1hj112pfp9hyp85y35rzrl2j"; depends=[curl dplyr DT httr jsonlite rjsoncons shiny]; }; + cellxgenedp = derive2 { name="cellxgenedp"; version="1.4.1"; sha256="09dpynmm1xg7hgiq5jvxvrwalaks0p7cim1cfa737wzflspz3pmj"; depends=[curl dplyr DT httr jsonlite rjsoncons shiny]; }; censcyt = derive2 { name="censcyt"; version="1.8.0"; sha256="0ql7k42z96swaizags3nijx92zjc64whi3c8a26hvjykpdhrzxwv"; depends=[BiocParallel broom_mixed diffcyt dirmult dplyr edgeR fitdistrplus lme4 magrittr MASS mice multcomp purrr rlang S4Vectors stringr SummarizedExperiment survival tibble tidyr]; }; cfDNAPro = derive2 { name="cfDNAPro"; version="1.6.0"; sha256="05vbwdcgmffzldfk6g882lbfrygw25nhx6fgrbadphdw72q1ynrn"; depends=[BiocGenerics BSgenome_Hsapiens_NCBI_GRCh38 BSgenome_Hsapiens_UCSC_hg19 BSgenome_Hsapiens_UCSC_hg38 dplyr GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 IRanges magrittr plyranges quantmod rlang Rsamtools stringr tibble]; }; cfTools = derive2 { name="cfTools"; version="1.0.0"; sha256="1ggvcsnqhf69559a3axpdszm41mvg60138lh2xlnsm0642f648wy"; depends=[basilisk BH GenomicRanges R_utils Rcpp]; }; @@ -1252,7 +1255,7 @@ in with self; { clstutils = derive2 { name="clstutils"; version="1.48.0"; sha256="16sk150yibqvz0nx2n5vivxmd56913myyb2j4jxcf5fg8vxrr1f2"; depends=[ape clst lattice rjson RSQLite]; }; clustComp = derive2 { name="clustComp"; version="1.28.0"; sha256="0i153cf3qavg6pxs5k8g6jrz2mp26fj1qrywrjwrzaf4h575dwk7"; depends=[sm]; }; clusterExperiment = derive2 { name="clusterExperiment"; version="2.20.0"; sha256="0h22zh6jpd2wsh6b9rnrmx8897aqlrsnw82kwphx8lay4r1vv706"; depends=[ape BiocGenerics BiocSingular cluster DelayedArray edgeR HDF5Array howmany kernlab limma locfdr Matrix matrixStats mbkmeans NMF phylobase pracma RColorBrewer Rcpp S4Vectors scales SingleCellExperiment stringr SummarizedExperiment zinbwave]; }; - clusterProfiler = derive2 { name="clusterProfiler"; version="4.8.2"; sha256="0iijby2j9i6sbdc3iwhqqb8xlz25k3dpiyq91p7yybggpr2p1nw4"; depends=[AnnotationDbi DOSE downloader dplyr enrichplot GO_db GOSemSim gson magrittr plyr qvalue rlang tidyr yulab_utils]; }; + clusterProfiler = derive2 { name="clusterProfiler"; version="4.8.3"; sha256="1kihrpa8cb2bqk5dck0w6yzgfpl72qxlrxwpidg1ar27q3ivz8w3"; depends=[AnnotationDbi DOSE downloader dplyr enrichplot GO_db GOSemSim gson magrittr plyr qvalue rlang tidyr yulab_utils]; }; clusterStab = derive2 { name="clusterStab"; version="1.72.0"; sha256="0imx4jfi2cjriy30cvmskfhkyrjn6s4wj6sw33v9zkqracfxnhzk"; depends=[Biobase]; }; clustifyr = derive2 { name="clustifyr"; version="1.12.0"; sha256="0i6gs7mvxav8wpj4bsslcgdwlaih2p1f5yfwdgbi3n36b6giirv5"; depends=[cowplot dplyr entropy fgsea ggplot2 httr Matrix matrixStats proxy readr rlang S4Vectors scales SingleCellExperiment stringr SummarizedExperiment tibble tidyr]; }; cmapR = derive2 { name="cmapR"; version="1.12.0"; sha256="1pkigc8a0a0cjn0hxirjr50a1zs7ig3crm7rrs2gw0zjvzvkmsgc"; depends=[data_table flowCore matrixStats rhdf5 SummarizedExperiment]; }; @@ -1265,7 +1268,7 @@ in with self; { coRdon = derive2 { name="coRdon"; version="1.18.0"; sha256="1qisxv0i05dcsf9nxgbwhswzxrckrabz5jzh78fnh7x9hh7rsd62"; depends=[Biobase Biostrings data_table dplyr ggplot2 purrr stringr]; }; codelink = derive2 { name="codelink"; version="1.68.0"; sha256="0gsdkzdgi4l34i9jk4b2h10rniwm0w0h7m5p1i8v20j7dlnihhs4"; depends=[annotate Biobase BiocGenerics limma]; }; cogena = derive2 { name="cogena"; version="1.34.0"; sha256="1gfkbj3b7j1hd0y0s5fp00hq1lllxhpirjaxphhhaj8vhvh5xpy8"; depends=[amap apcluster Biobase biwt class cluster corrplot devtools doParallel dplyr fastcluster foreach ggplot2 gplots kohonen mclust reshape2 stringr tibble tidyr]; }; - cogeqc = derive2 { name="cogeqc"; version="1.4.0"; sha256="1v6vxcwwh6v4xwka1h0pyp7i7z7xs2k06qbx8b3hy1v9v2bkqd50"; depends=[Biostrings ggbeeswarm ggplot2 ggtree igraph jsonlite patchwork reshape2 rlang scales]; }; + cogeqc = derive2 { name="cogeqc"; version="1.4.1"; sha256="02gh0ky3fzkdzg0j09v31l7zcmncx0i7a39filfydnky69i362l2"; depends=[Biostrings ggbeeswarm ggplot2 ggtree igraph jsonlite patchwork reshape2 rlang scales]; }; cola = derive2 { name="cola"; version="2.6.0"; sha256="104l0dnav1z9kk2r1a0hyqcm230cgpkcap4dng9a0r6vsd5bvz8k"; depends=[BiocGenerics brew circlize clue cluster ComplexHeatmap crayon digest doParallel doRNG eulerr foreach GetoptLong GlobalOptions httr impute irlba knitr markdown matrixStats mclust microbenchmark png RColorBrewer Rcpp skmeans xml2]; }; comapr = derive2 { name="comapr"; version="1.4.0"; sha256="0w4jajd088bxf664ajs5cfgq14hn5xfdsydsrsnb97jv8jhjxc19"; depends=[BiocParallel circlize dplyr foreach GenomeInfoDb GenomicRanges ggplot2 gridExtra Gviz IRanges Matrix plotly plyr RColorBrewer reshape2 rlang S4Vectors scales SummarizedExperiment tidyr]; }; combi = derive2 { name="combi"; version="1.12.1"; sha256="1ax4vsj0pwm5xzp01mgmm8vx2w6sz8fl0fiwwbkrgnbnmkd2gfjh"; depends=[alabama BB Biobase cobs DBI ggplot2 limma Matrix nleqslv phyloseq reshape2 SummarizedExperiment tensor vegan]; }; @@ -1317,7 +1320,7 @@ in with self; { cytofQC = derive2 { name="cytofQC"; version="1.0.0"; sha256="0isfngah9bziwfbrlqqcg7h57cwpphxwv52xvgjvd970ch9bl598"; depends=[CATALYST e1071 EZtune flowCore gbm ggplot2 hrbrthemes matrixStats randomForest rmarkdown S4Vectors SingleCellExperiment ssc SummarizedExperiment]; }; cytolib = derive2 { name="cytolib"; version="2.12.1"; sha256="0mfv259k92vz0g7zv8zir2av2nlmx6na1f6q9zyj24s18m7mrkqz"; depends=[BH Rhdf5lib RProtoBufLib]; }; cytomapper = derive2 { name="cytomapper"; version="1.12.0"; sha256="1z3ic6w4pkysw546kh0ybwyj13wdd1a7ixa83ws200aydryybjmc"; depends=[BiocParallel DelayedArray EBImage ggbeeswarm ggplot2 HDF5Array matrixStats nnls raster RColorBrewer rhdf5 S4Vectors shiny shinydashboard SingleCellExperiment SpatialExperiment SummarizedExperiment svglite svgPanZoom viridis]; }; - cytoviewer = derive2 { name="cytoviewer"; version="1.0.0"; sha256="0i1rklm9s9vlk8mbnzsvm2837rk44sn9zy1pch983q12cjg63iw6"; depends=[archive colourpicker cytomapper EBImage RColorBrewer S4Vectors shiny shinycssloaders shinydashboard SingleCellExperiment SummarizedExperiment svglite svgPanZoom viridis]; }; + cytoviewer = derive2 { name="cytoviewer"; version="1.0.1"; sha256="1ckgwp0gxiv92dd4g25b4fq9mk3xc27lslap0d165a0p2km6jzfl"; depends=[archive colourpicker cytomapper EBImage RColorBrewer S4Vectors shiny shinycssloaders shinydashboard SingleCellExperiment SummarizedExperiment svglite svgPanZoom viridis]; }; dStruct = derive2 { name="dStruct"; version="1.6.0"; sha256="1bcmv30gj2rfzgwk9ncpbn5z0ra5jxpm94npw9nd6lz8gf6qmm74"; depends=[ggplot2 IRanges purrr reshape2 rlang S4Vectors zoo]; }; daMA = derive2 { name="daMA"; version="1.72.0"; sha256="0z4y57hna312pkhkchair8calm7wl40rx8lcm8i6h1789hba063d"; depends=[MASS]; }; dada2 = derive2 { name="dada2"; version="1.28.0"; sha256="1vxy2106rzygy0dr38wmw84zrqp9gsvaphliikdmhx0n2gv6xhd1"; depends=[BiocGenerics Biostrings ggplot2 IRanges Rcpp RcppParallel reshape2 ShortRead XVector]; }; @@ -1354,17 +1357,17 @@ in with self; { dir_expiry = derive2 { name="dir.expiry"; version="1.8.0"; sha256="1vccq28734s7zk7pc7i9zq4rzbi373xqqvgkzamjpii36phkdmlw"; depends=[filelock]; }; discordant = derive2 { name="discordant"; version="1.24.0"; sha256="1c3qfj6yx6pnpjzm6lgs4ark3dlw21amkxcnrzqi4qxdl2r5jkgn"; depends=[Biobase biwt dplyr gtools MASS Rcpp]; }; distinct = derive2 { name="distinct"; version="1.12.2"; sha256="1yzsnjcwh4l8iy7hx9zhgx2kxdfvszc60dahgd1sx6mmybcg89zv"; depends=[doParallel doRNG foreach ggplot2 limma Matrix Rcpp RcppArmadillo Rfast scater SingleCellExperiment SummarizedExperiment]; }; - dittoSeq = derive2 { name="dittoSeq"; version="1.12.0"; sha256="0g5xxzd2xvh0m1fmyzzriwnrq1ckcmb95h9yl60h5w3c3ph22438"; depends=[colorspace cowplot ggplot2 ggrepel ggridges gridExtra pheatmap reshape2 S4Vectors SingleCellExperiment SummarizedExperiment]; }; + dittoSeq = derive2 { name="dittoSeq"; version="1.12.2"; sha256="13z7adkadcf405hk0x2ypjbm05465m5qzsvs1fb46mkr1fd9c822"; depends=[colorspace cowplot ggplot2 ggrepel ggridges gridExtra pheatmap reshape2 S4Vectors SingleCellExperiment SummarizedExperiment]; }; divergence = derive2 { name="divergence"; version="1.16.0"; sha256="1h212zjav0m4739mrshnp3ghnq0cr66knv5ihn6fy3grf00i1v9k"; depends=[SummarizedExperiment]; }; dks = derive2 { name="dks"; version="1.46.0"; sha256="1cbqcg7fk27y8y1hbfwz9vj6sgvygnmg855h9swlr2mq5kaka5ig"; depends=[cubature]; }; - dmrseq = derive2 { name="dmrseq"; version="1.20.0"; sha256="1xj23dqvmxi1sn4qn4zwvn9ggv128kr3gxmd7906463s9ap8qjja"; depends=[AnnotationHub annotatr BiocParallel bsseq bumphunter DelayedMatrixStats GenomeInfoDb GenomicRanges ggplot2 IRanges locfit matrixStats nlme outliers RColorBrewer rtracklayer S4Vectors]; }; + dmrseq = derive2 { name="dmrseq"; version="1.20.1"; sha256="1lxrirgy42xnpdj7b2nrabbki33an8ri6j1mgxp3jn4h0a88c280"; depends=[AnnotationHub annotatr BiocParallel bsseq bumphunter DelayedMatrixStats GenomeInfoDb GenomicRanges ggplot2 IRanges locfit matrixStats nlme outliers RColorBrewer rtracklayer S4Vectors]; }; doppelgangR = derive2 { name="doppelgangR"; version="1.28.1"; sha256="0sbwqrn4j364wj8j1s857hvxi2hch0cgm84h71sy6hmg7p5jdnvf"; depends=[Biobase BiocParallel digest impute mnormt SummarizedExperiment sva]; }; doseR = derive2 { name="doseR"; version="1.16.0"; sha256="1as6sinbry3ai8wlzrdpr8zfd4c9cyqlbwg0hc4ii4lvnykbm5hz"; depends=[digest edgeR lme4 matrixStats mclust RUnit S4Vectors SummarizedExperiment]; }; doubletrouble = derive2 { name="doubletrouble"; version="1.0.0"; sha256="0w82sgf7c86v3ir771a332x0ab09z517jvp43xx2chsbwahzyk1d"; depends=[Biostrings GenomicRanges ggplot2 mclust MSA2dist syntenet]; }; dpeak = derive2 { name="dpeak"; version="1.12.0"; sha256="1fx2rrcqmjckk5kk3mfa56b1393b2c8sf566q95d8zmlsvkl03w5"; depends=[BSgenome IRanges MASS Rcpp]; }; drawProteins = derive2 { name="drawProteins"; version="1.20.0"; sha256="15vxi4a8bm65s6ba7kyyr64l4k7frwa6l06537423ac245j7nkwl"; depends=[dplyr ggplot2 httr readr tidyr]; }; drugTargetInteractions = derive2 { name="drugTargetInteractions"; version="1.8.0"; sha256="0ll9fdfnvr8rbm54z1jf5w6b3dizm8fhzladnlc6xx5ysldasci3"; depends=[AnnotationFilter BiocFileCache biomaRt dplyr ensembldb rappdirs RSQLite S4Vectors UniProt_ws]; }; - dupRadar = derive2 { name="dupRadar"; version="1.30.0"; sha256="0gda6nx42xsskzpn55yj877703zmn1al5qrpjb0xyiw0ayjdg6d2"; depends=[KernSmooth Rsubread]; }; + dupRadar = derive2 { name="dupRadar"; version="1.30.3"; sha256="05j8ffdsg38rxpqxmrb154qdba1jlnhsfjkxgzs6fpkvcggp06g5"; depends=[KernSmooth Rsubread]; }; dyebias = derive2 { name="dyebias"; version="1.60.0"; sha256="1l4sk2hzghr0b983ki2jzr9myyy62pcz104vblql48jg6pxv28gk"; depends=[Biobase marray]; }; easier = derive2 { name="easier"; version="1.6.3"; sha256="1b8grnh0srla1pxln88bxg0n4z2ri6qjp4qi6f4d14mwdsylkfiy"; depends=[BiocParallel coin decoupleR DESeq2 dorothea dplyr easierData ggplot2 ggpubr ggrepel magrittr matrixStats progeny quantiseqr reshape2 rlang ROCR rstatix tibble tidyr]; }; easyRNASeq = derive2 { name="easyRNASeq"; version="2.36.0"; sha256="1cax4k6rppk0kxwannf0ar17jx1pa7lp52a398skqkhy87s29dbp"; depends=[Biobase BiocFileCache BiocGenerics BiocParallel biomaRt Biostrings edgeR GenomeInfoDb genomeIntervals GenomicAlignments GenomicRanges IRanges locfit LSD rappdirs Rsamtools S4Vectors ShortRead SummarizedExperiment]; }; @@ -1378,14 +1381,14 @@ in with self; { eisaR = derive2 { name="eisaR"; version="1.12.0"; sha256="0g2zg8y0mdn0nn1jw5dlvm2245913fmw7lbgymkwlihf5xm8s345"; depends=[BiocGenerics edgeR GenomicRanges IRanges limma S4Vectors SummarizedExperiment]; }; enhancerHomologSearch = derive2 { name="enhancerHomologSearch"; version="1.6.1"; sha256="081b6d8m4kq4bsrxs8pwg58lwrifd2cc2ymkqcv491xnfabr3ais"; depends=[BiocFileCache BiocGenerics BiocParallel Biostrings BSgenome GenomeInfoDb GenomicRanges httr IRanges jsonlite Matrix motifmatchr Rcpp rtracklayer S4Vectors]; }; enrichTF = derive2 { name="enrichTF"; version="1.16.0"; sha256="15k7vy02270ygl354wxy7dsx4w2qx6bidqyhsb1dcamhy2z11403"; depends=[BiocGenerics BSgenome clusterProfiler GenomeInfoDb GenomicRanges ggplot2 ggpubr heatmap3 IRanges JASPAR2018 magrittr motifmatchr pipeFrame R_utils rmarkdown rtracklayer S4Vectors TFBSTools]; }; - enrichplot = derive2 { name="enrichplot"; version="1.20.0"; sha256="10vmlw58hgzcpv2hlxk9ircza889vs9z01z575633qj0ivsczh0z"; depends=[aplot DOSE ggnewscale ggplot2 ggraph ggtree GOSemSim igraph magrittr plyr purrr RColorBrewer reshape2 rlang scatterpie shadowtext yulab_utils]; }; + enrichplot = derive2 { name="enrichplot"; version="1.20.3"; sha256="11hgxs42wvirv6b9ywr2jb51s67k4r0pm21dkvm7xjbsbarlkhmh"; depends=[aplot DOSE ggfun ggnewscale ggplot2 ggraph ggtree GOSemSim igraph magrittr plyr purrr RColorBrewer reshape2 rlang scatterpie shadowtext yulab_utils]; }; ensemblVEP = derive2 { name="ensemblVEP"; version="1.42.0"; sha256="0s743p10cf1vjw8b44qy6cwx77ykkq931sil1cv9km278zpkp3b5"; depends=[BiocGenerics Biostrings GenomeInfoDb GenomicRanges S4Vectors SummarizedExperiment VariantAnnotation]; }; - ensembldb = derive2 { name="ensembldb"; version="2.24.0"; sha256="0rl5ix755055i95y5xfb4zv5gih2gkqwqia1r1b3yx12z5ybvkc6"; depends=[AnnotationDbi AnnotationFilter Biobase BiocGenerics Biostrings curl DBI GenomeInfoDb GenomicFeatures GenomicRanges IRanges ProtGenerics Rsamtools RSQLite rtracklayer S4Vectors]; }; + ensembldb = derive2 { name="ensembldb"; version="2.24.1"; sha256="1x73lln0rlnypl8iia54srl3wrazs94f8rspmjsaqsxwknkym319"; depends=[AnnotationDbi AnnotationFilter Biobase BiocGenerics Biostrings curl DBI GenomeInfoDb GenomicFeatures GenomicRanges IRanges ProtGenerics Rsamtools RSQLite rtracklayer S4Vectors]; }; epiNEM = derive2 { name="epiNEM"; version="1.24.0"; sha256="1c13mrw9if1v3gx8c662p48prx5hy8ndgs35ma4dv93kkgqxg9i2"; depends=[BoolNet e1071 graph gtools igraph latex2exp lattice latticeExtra minet mnem pcalg RColorBrewer]; }; - epialleleR = derive2 { name="epialleleR"; version="1.8.0"; sha256="1addbbxifj5ksrnxn7i3kfc1bywpd9zkxl4ky6hbswpjygv4b9gp"; depends=[BH BiocGenerics data_table GenomeInfoDb GenomicRanges Rcpp Rhtslib stringi SummarizedExperiment VariantAnnotation zlibbioc]; }; + epialleleR = derive2 { name="epialleleR"; version="1.8.1"; sha256="1jjydv6f10zdrk5fx54a7iy9fl5rk6j3wk3i0i7zzd4nsk7m8rpz"; depends=[BH BiocGenerics data_table GenomeInfoDb GenomicRanges Rcpp Rhtslib stringi SummarizedExperiment VariantAnnotation zlibbioc]; }; epidecodeR = derive2 { name="epidecodeR"; version="1.8.0"; sha256="19422k6v9xc1gq3hw2mbqcgp3jdllmkjrcqsac0b02i4ly4yad8h"; depends=[dplyr EnvStats GenomicRanges ggplot2 ggpubr IRanges rstatix rtracklayer]; }; epigenomix = derive2 { name="epigenomix"; version="1.40.0"; sha256="1mgxc3bsgh93ij8qpa4mr4pcc3p0avzhwyk68hzc5k48c7f9n782"; depends=[beadarray Biobase BiocGenerics GenomeInfoDb GenomicRanges IRanges MCMCpack Rsamtools S4Vectors SummarizedExperiment]; }; - epigraHMM = derive2 { name="epigraHMM"; version="1.8.2"; sha256="1gw13i0sjvd1a5krfnk9vgp55mhq6dlinpprpqj7rg1gp5h2d76w"; 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="1.8.3"; sha256="1kcr6rkh3bn2j93i249mk0jsykf9cbl8h50ly60jsg1h62xqqswg"; 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]; }; epimutacions = derive2 { name="epimutacions"; version="1.4.0"; sha256="079mkdri07zhx41gd78x88kq0isj6lahijbxr6whc8p5g8qk6p3f"; 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="1.6.0"; sha256="1rnc7vnm6n6f88zncag4x3m2z8nn28r8mjh9cdgr2i2p177cipav"; depends=[BiocGenerics GenomicRanges IRanges plotrix S4Vectors SummarizedExperiment]; }; epistasisGA = derive2 { name="epistasisGA"; version="1.2.1"; sha256="1rs3m4jc9lmwzxg20mknbdrlpnrm0z54ldi5xywmpzyf382r8lka"; depends=[batchtools BH bigmemory BiocParallel data_table ggplot2 igraph matrixStats qgraph Rcpp RcppArmadillo survival]; }; @@ -1433,7 +1436,7 @@ in with self; { flowCore = derive2 { name="flowCore"; version="2.12.2"; sha256="1z3xsp1ymvdjhwcj5mkhl1d586rlr5i8vji9y5gs595w3naa4r0h"; depends=[BH Biobase BiocGenerics cpp11 cytolib matrixStats Rcpp RProtoBufLib S4Vectors]; }; flowCut = derive2 { name="flowCut"; version="1.10.0"; sha256="0gfnc45yg6m6i4gkag65bkc3569441rrbyhi0xbxabrkb8m9a3f0"; depends=[Cairo e1071 flowCore flowDensity]; }; flowCyBar = derive2 { name="flowCyBar"; version="1.36.0"; sha256="0rl1xmil6197pkmwkmvcvscsw7b0bp4ljrj3zjrihpjjq5x7fivw"; depends=[gplots vegan]; }; - flowDensity = derive2 { name="flowDensity"; version="1.34.0"; sha256="1g71sng0f53z6i8vsfirb0qpxadd4vcrmhcfndh88avphrp2i1i5"; depends=[car flowCore flowViz flowWorkspace gplots RFOC rgeos sp]; }; + flowDensity = derive2 { name="flowDensity"; version="1.34.0"; sha256="1g71sng0f53z6i8vsfirb0qpxadd4vcrmhcfndh88avphrp2i1i5"; depends=[car flowCore flowViz flowWorkspace gplots RFOC sp]; }; flowFP = derive2 { name="flowFP"; version="1.58.0"; sha256="1c7j84ax36ybxs7qpkcnxggv4ajzh4dip76caaq7qw8fyyd9cdy4"; depends=[Biobase BiocGenerics flowCore flowViz]; }; flowGate = derive2 { name="flowGate"; version="1.0.0"; sha256="0wkmpzrbv8bkh9b7glgh5zzncij4511wx5a59g4i5q2w9c3vw8bc"; depends=[BiocManager dplyr flowCore flowWorkspace ggcyto ggplot2 purrr rlang shiny tibble]; }; flowGraph = derive2 { name="flowGraph"; version="1.8.0"; sha256="1kx01vzh5qrpsdqqmrkdjfkcvb1bilbvbx632dd4qdcsxizmj3bb"; depends=[data_table effsize furrr future ggiraph ggplot2 ggrepel gridExtra htmlwidgets igraph Matrix matrixStats purrr Rdpack stringi stringr visNetwork]; }; @@ -1450,7 +1453,7 @@ in with self; { flowTrans = derive2 { name="flowTrans"; version="1.52.0"; sha256="1mmi75n957wlmp8x34p1h4giq89g20ahyvzrvf582w5662id9k34"; depends=[flowClust flowCore flowViz]; }; flowVS = derive2 { name="flowVS"; version="1.32.0"; sha256="1qm6qs8rs3qc3x9nj3kn7qrnfaqzdw5rj7bzfkhfvvxcsnmgmch8"; depends=[flowCore flowStats flowViz]; }; flowViz = derive2 { name="flowViz"; version="1.64.0"; sha256="0y16hzadpr5c99cwkphc07vh6lypgfk5nacbmn7mmrw01b3gbk67"; depends=[Biobase flowCore hexbin IDPmisc KernSmooth lattice latticeExtra MASS RColorBrewer]; }; - flowWorkspace = derive2 { name="flowWorkspace"; version="4.12.1"; sha256="0mn9j0zxhqmiqbb5zgs87d1jrrm020r5yy2cp7c0ghb2l7c843zb"; depends=[BH Biobase BiocGenerics cpp11 cytolib data_table DelayedArray dplyr flowCore ggplot2 graph matrixStats ncdfFlow RBGL Rgraphviz Rhdf5lib RProtoBufLib S4Vectors scales XML]; }; + flowWorkspace = derive2 { name="flowWorkspace"; version="4.12.2"; sha256="1g1hym2anysgy7v46fnnxyzac3wzi1713vlih2gqzi23k8r2xx26"; depends=[BH Biobase BiocGenerics cpp11 cytolib data_table DelayedArray dplyr flowCore ggplot2 graph matrixStats ncdfFlow RBGL Rgraphviz Rhdf5lib RProtoBufLib S4Vectors scales XML]; }; flowcatchR = derive2 { name="flowcatchR"; version="1.34.0"; sha256="159j5izrgmc8mqn48aq9n4da07mw375yp62g9rdml266wvyvvm9f"; depends=[abind BiocParallel colorRamps EBImage plotly shiny]; }; fmcsR = derive2 { name="fmcsR"; version="1.42.0"; sha256="0ci77gbz93i3s2j2gjp7y3ssn6bcdcmqnl23smnjai7qjmln64dp"; depends=[BiocGenerics ChemmineR RUnit]; }; fmrs = derive2 { name="fmrs"; version="1.10.0"; sha256="17bwvymh1vk6xh1631dvkjxkap9b2azyypncjyvg6s5i9y0dabz3"; depends=[survival]; }; @@ -1480,7 +1483,7 @@ in with self; { geneXtendeR = derive2 { name="geneXtendeR"; version="1.26.0"; sha256="0dba80hvvwm3yvr1jg2c168wxq53clr63wjf5cdfaig8i40z378m"; depends=[AnnotationDbi BiocStyle data_table dplyr GO_db networkD3 org_Rn_eg_db RColorBrewer rtracklayer SnowballC tm wordcloud]; }; genefilter = derive2 { name="genefilter"; version="1.82.1"; sha256="1wpg8banz6s6smycfqf9hqryp4kf2gs069s7npyvpq53wy0kxyny"; depends=[annotate AnnotationDbi Biobase MatrixGenerics survival]; }; genefu = derive2 { name="genefu"; version="2.32.0"; sha256="0jiirmi6wb6zr5spmn8nrqcrk3ks8hhs1nrm6aiwrky26rn1szrv"; depends=[AIMS amap biomaRt iC10 impute limma mclust survcomp]; }; - geneplast = derive2 { name="geneplast"; version="1.26.0"; sha256="11rjyj2qbbqqjw8s1j5rjgx1h6rzypdnv47vx5xml46qd97ks7fm"; depends=[ape data_table igraph snow]; }; + geneplast = derive2 { name="geneplast"; version="1.26.1"; sha256="1q61244dwf68h05q9ml5d9fs2zcxrl5fgi504f3pz83a426w1dk4"; depends=[ape data_table igraph snow]; }; geneplotter = derive2 { name="geneplotter"; version="1.78.0"; sha256="03x90l7rvxk0z03p5immqbyyhiygi3mkik636al1cjdcxl9dr5f8"; depends=[annotate AnnotationDbi Biobase BiocGenerics lattice RColorBrewer]; }; genoCN = derive2 { name="genoCN"; version="1.52.0"; sha256="0dlb3bxbmj9pgvb2zs4q3iy1vpnafwd3qnxy951qm2ln08ksidhy"; depends=[]; }; genomation = derive2 { name="genomation"; version="1.32.0"; sha256="0y6a2qxxp5mnkllcq46j00069z22ixnrbkd15s007a35lhkibz21"; depends=[Biostrings BSgenome data_table GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 gridBase impute IRanges matrixStats plotrix plyr Rcpp readr reshape2 Rsamtools rtracklayer S4Vectors seqPattern]; }; @@ -1497,7 +1500,7 @@ in with self; { ggmsa = derive2 { name="ggmsa"; version="1.6.0"; sha256="077wx2l4mg95zkx5728ajnr9qm70r6rp2d426w2inwsfl99prqdx"; depends=[aplot Biostrings dplyr ggalt ggforce ggplot2 ggtree magrittr R4RNA RColorBrewer seqmagick statebins tidyr]; }; ggspavis = derive2 { name="ggspavis"; version="1.6.0"; sha256="0df7xgp952a6v4qpby4yqxa473i7w732imv9lc1svnin9184ip8m"; depends=[ggplot2 ggside SingleCellExperiment SpatialExperiment SummarizedExperiment]; }; ggtree = derive2 { name="ggtree"; version="3.8.2"; sha256="0l8llnvmg8k5qgag6vfgx1gdv0x46p3ypfz5apv23qhlbx4jfjja"; depends=[ape aplot cli dplyr ggfun ggplot2 magrittr purrr rlang scales tidyr tidytree treeio yulab_utils]; }; - ggtreeDendro = derive2 { name="ggtreeDendro"; version="1.2.0"; sha256="0c82nkp5iv9xib22j3zlh009vg9m94jh89pryx07k4j22r9gjdci"; depends=[ggplot2 ggtree tidytree]; }; + ggtreeDendro = derive2 { name="ggtreeDendro"; version="1.2.1"; sha256="0v54lp1b2d2nga7rspg74x3fmbywcmsx63cjid0n23l0zbyb3vgb"; depends=[ggplot2 ggtree tidytree]; }; ggtreeExtra = derive2 { name="ggtreeExtra"; version="1.10.0"; sha256="19xikly6ksh03kgpz35wj2d2gdbpikhrk71ahj9ghhkmlwdyjbcr"; depends=[cli ggnewscale ggplot2 ggtree magrittr rlang tidytree]; }; girafe = derive2 { name="girafe"; version="1.52.0"; sha256="0cddz4jm063fgjnxzzsdnllaydfc2zxpyp8by2cacy2qzx95s8qy"; depends=[Biobase BiocGenerics Biostrings genomeIntervals intervals IRanges Rsamtools S4Vectors ShortRead]; }; glmGamPoi = derive2 { name="glmGamPoi"; version="1.12.2"; sha256="0d6q8vn8z90k8ffskcn9jmgg5x5pfb3wjv67bqskasy38inn1zg7"; depends=[beachmat BiocGenerics DelayedArray DelayedMatrixStats HDF5Array MatrixGenerics matrixStats Rcpp RcppArmadillo rlang SingleCellExperiment SummarizedExperiment vctrs]; }; @@ -1565,7 +1568,7 @@ in with self; { idr2d = derive2 { name="idr2d"; version="1.14.0"; sha256="0inj3lwcrpx9wyxvbsijsr5l6lzjm5mxf23khsswfl1lc9c0bqhn"; depends=[dplyr futile_logger GenomeInfoDb GenomicRanges ggplot2 idr IRanges magrittr reticulate scales stringr]; }; igvR = derive2 { name="igvR"; version="1.20.0"; sha256="0kfsl2w3a9bycp7baha1q5a1n7hfzp6scw1hv1kjsmvc6f5mszzh"; depends=[BiocGenerics BrowserViz GenomicAlignments GenomicRanges httpuv httr RColorBrewer rtracklayer VariantAnnotation]; }; illuminaio = derive2 { name="illuminaio"; version="0.42.0"; sha256="190i3b9qmh26bic1lzi54mw4p1nrg57qijl1pg6b29w3i6srq692"; depends=[base64]; }; - imcRtools = derive2 { name="imcRtools"; version="1.6.3"; sha256="1i57blfbbiklahi4gxa3hs7fqwc1ryl1yw2y46jf59icaf4sx41i"; depends=[abind BiocNeighbors BiocParallel concaveman cytomapper data_table distances dplyr DT EBImage ggplot2 ggraph igraph magrittr MatrixGenerics pheatmap readr RTriangle S4Vectors scuttle sf SingleCellExperiment SpatialExperiment stringr SummarizedExperiment tidygraph tidyselect viridis vroom]; }; + imcRtools = derive2 { name="imcRtools"; version="1.6.5"; sha256="0x2mzz8s1fhjw2kxggjxsaj1m1m0bss7isiqgizfwsslwqsn9k1j"; depends=[abind BiocNeighbors BiocParallel concaveman cytomapper data_table distances dplyr DT EBImage ggplot2 ggraph igraph magrittr MatrixGenerics pheatmap readr RTriangle S4Vectors scuttle sf SingleCellExperiment SpatialExperiment stringr SummarizedExperiment tidygraph tidyselect viridis vroom]; }; immunoClust = derive2 { name="immunoClust"; version="1.32.0"; sha256="1pd26qli5bj05qivwppz5rpvzm28wp7aqymsg381yg7kzyqlqjdx"; depends=[flowCore lattice]; }; immunotation = derive2 { name="immunotation"; version="1.8.0"; sha256="1pdzs1pv8pddcycacbhrswf73kbhamxw8fckapgf81zxav2sb2ml"; depends=[curl ggplot2 maps ontologyIndex readr rlang rvest stringr tidyr xml2]; }; impute = derive2 { name="impute"; version="1.74.1"; sha256="0nz8ggzk2g5w20yyhp6av6hy69kbmg3ncfpq9ppmq6p5a0msx92l"; depends=[]; }; @@ -1589,7 +1592,7 @@ in with self; { kissDE = derive2 { name="kissDE"; version="1.20.0"; sha256="1dijdss2qakvgxshcpd5n95zly5q4b7fpkvxh265g8fj4b3hzf62"; depends=[ade4 aods3 Biobase DESeq2 doParallel DSS DT factoextra foreach ggplot2 gplots matrixStats shiny shinycssloaders]; }; lapmix = derive2 { name="lapmix"; version="1.66.0"; sha256="1kymd9y1fy6wmkmsb3xi16hzacwb8myj012ksqdflpx679g2lya0"; depends=[Biobase]; }; ldblock = derive2 { name="ldblock"; version="1.30.0"; sha256="18gqmwwi1i4gndqljy809n5zzx38agawxxwhlknpas6k2iskd1xq"; depends=[BiocGenerics httr Matrix rlang]; }; - lefser = derive2 { name="lefser"; version="1.10.0"; sha256="0wi70b4k7s0xj7bh46s0x0fckqc5qspzq8k4k913vg6cnhqgw2dd"; depends=[coin ggplot2 MASS SummarizedExperiment]; }; + lefser = derive2 { name="lefser"; version="1.10.1"; sha256="1ifmbbsbyzcyvjni9ww27c9qsqliv7vj2rv9mg9c7gnqgbg6h2c4"; depends=[coin ggplot2 MASS S4Vectors SummarizedExperiment]; }; les = derive2 { name="les"; version="1.50.0"; sha256="034254qz2kh4v1hnvriacnmsfdy2vhpr2xag939nq2v13xn23sic"; depends=[boot fdrtool gplots RColorBrewer]; }; levi = derive2 { name="levi"; version="1.18.0"; sha256="1ff8w4bh2f488b2v9cgsdmc98xy33zfj1ffladdm6bhsmfqkgbsv"; depends=[colorspace dplyr DT ggplot2 httr igraph knitr RColorBrewer Rcpp reshape2 rmarkdown shiny shinydashboard shinyjs testthat xml2]; }; lfa = derive2 { name="lfa"; version="2.0.11"; sha256="0x169fxwlccsqwj1bpviaky3hfr0zdwsdrlgfvrb4j6j95qfgnns"; depends=[corpcor RSpectra]; }; @@ -1598,7 +1601,7 @@ in with self; { lineagespot = derive2 { name="lineagespot"; version="1.4.0"; sha256="1mmypd4rjdai3iyyp0sx1wk732kripjrimx1dby2xw397z1pszb4"; depends=[data_table httr MatrixGenerics stringr SummarizedExperiment VariantAnnotation]; }; lionessR = derive2 { name="lionessR"; version="1.14.0"; sha256="0yfznjza95z18r62m35ck4f2sxyc12ip912m6p9zwfqviaczb1si"; depends=[S4Vectors SummarizedExperiment]; }; lipidr = derive2 { name="lipidr"; version="2.14.1"; sha256="1yqpidlgdps3657hx6kwz6nv9wf6p4sjl45jqrn8pk9jx1xcbn13"; depends=[data_table dplyr fgsea forcats ggplot2 imputeLCMD limma magrittr rlang ropls S4Vectors SummarizedExperiment tidyr]; }; - lisaClust = derive2 { name="lisaClust"; version="1.8.0"; sha256="18yqn9cjyj86inphsvs3c02hi9vb1x69cb67mmmx556ywyh1a817"; depends=[BiocGenerics BiocParallel class concaveman data_table dplyr ggplot2 pheatmap purrr S4Vectors SingleCellExperiment SpatialExperiment spatstat_explore spatstat_geom spicyR SummarizedExperiment tidyr]; }; + lisaClust = derive2 { name="lisaClust"; version="1.8.2"; sha256="0mzf5b3qs4p86ypsyrkpd03vkyii35aivkrp4l5j82ds9jzb5hn1"; depends=[BiocGenerics BiocParallel class concaveman data_table dplyr ggplot2 pheatmap purrr S4Vectors SingleCellExperiment SpatialExperiment spatstat_explore spatstat_geom spatstat_random spicyR SummarizedExperiment tidyr]; }; lmdme = derive2 { name="lmdme"; version="1.42.0"; sha256="1awnbfdfvlziik9nwp5xlpbhc7gp17q2z6sgilmrdmjx9cknbb41"; depends=[limma pls stemHypoxia]; }; loci2path = derive2 { name="loci2path"; version="1.20.0"; sha256="1z4qxr8zc0miinh05pnks7h7ysqybsixln51fp0gfrb499jlbkfp"; depends=[BiocParallel data_table GenomicRanges pheatmap RColorBrewer S4Vectors wordcloud]; }; logicFS = derive2 { name="logicFS"; version="2.20.0"; sha256="17sa4wr1zly8bj3fmqknxip6ss7q68f3bni20ckc9yljacdv24jx"; depends=[LogicReg mcbiopi survival]; }; @@ -1664,7 +1667,7 @@ in with self; { methylPipe = derive2 { name="methylPipe"; version="1.34.1"; sha256="1128i8q95dq1xwwx273pl0pzizarvbx2pgvhakw6sjb2ry5prw6d"; depends=[BiocGenerics Biostrings data_table GenomeInfoDb GenomicAlignments GenomicRanges gplots Gviz IRanges marray Rsamtools S4Vectors SummarizedExperiment]; }; methylSig = derive2 { name="methylSig"; version="1.12.0"; sha256="1k7nm84k870cqzr4dvi5vfz3sphs091l0a677kdk4gzs5nkg5818"; depends=[bsseq DelayedArray DelayedMatrixStats DSS GenomeInfoDb GenomicRanges IRanges S4Vectors]; }; methylclock = derive2 { name="methylclock"; version="1.6.0"; sha256="1l8a24xpf8a5n49zcnidv2jb22rjza80v1ysxa10689w27lhf8h7"; depends=[Biobase devtools dplyr dynamicTreeCut ExperimentHub ggplot2 ggpmisc ggpubr gridExtra impute methylclockData minfi PerformanceAnalytics planet preprocessCore quadprog Rcpp RPMM tibble tidyr tidyverse]; }; - methylscaper = derive2 { name="methylscaper"; version="1.8.4"; sha256="1n6v35n2x6lpphydll7s2x54q2lz8avwc6jjqpiwb7c3z74jwy7r"; depends=[BiocParallel Biostrings data_table Rfast seqinr seriation shiny shinyFiles shinyjs SummarizedExperiment]; }; + methylscaper = derive2 { name="methylscaper"; version="1.8.6"; sha256="1fs58fqxwlg85iwbn1hzwv93af737cab6wkx1dbm5sd059ks2dzp"; depends=[BiocParallel Biostrings data_table Rfast seqinr seriation shiny shinyFiles shinyjs SummarizedExperiment]; }; methylumi = derive2 { name="methylumi"; version="2.46.0"; sha256="1aa0pwjyp2p9a4mx4n4qw88ndgrj56p669yzdkd7hxhc3x55nzlf"; depends=[annotate AnnotationDbi Biobase BiocGenerics FDb_InfiniumMethylation_hg19 genefilter GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 illuminaio IRanges lattice matrixStats minfi reshape2 S4Vectors scales SummarizedExperiment]; }; mfa = derive2 { name="mfa"; version="1.22.0"; sha256="1rc88ilaqhnbachajc0nagmj865g9w8ny1n9n094qiad9j47nfh4"; depends=[Biobase coda dplyr ggmcmc ggplot2 magrittr MCMCglmm MCMCpack Rcpp tibble]; }; mgsa = derive2 { name="mgsa"; version="1.48.0"; sha256="08szkzkdqzll4ki75lvkkvpz6kcv54863cicw376z73fd3x4bwgd"; depends=[gplots]; }; @@ -1755,7 +1758,7 @@ in with self; { netresponse = derive2 { name="netresponse"; version="1.60.0"; sha256="192g4rcyazzxpimkqyxh5y1s1g3i2li4qskh5160yaxp4x31vs9n"; depends=[BiocStyle ggplot2 graph igraph mclust minet plyr qvalue RColorBrewer reshape2 Rgraphviz rmarkdown]; }; ngsReports = derive2 { name="ngsReports"; version="2.2.4"; sha256="0d5rd4gzwx266kqmg38fjyknfg4pmp6rp99l36f2f4wjmbyih32l"; depends=[BiocGenerics Biostrings checkmate dplyr DT forcats ggdendro ggplot2 jsonlite lifecycle lubridate pander patchwork plotly readr reshape2 rlang rmarkdown scales stringr tibble tidyr tidyselect zoo]; }; nnNorm = derive2 { name="nnNorm"; version="2.64.0"; sha256="19nywnq17bijxzxcpmmiq8q9jbjskzw2bi0g33zw3g9ksrg3d758"; depends=[marray nnet]; }; - nnSVG = derive2 { name="nnSVG"; version="1.4.1"; sha256="171c246cj610hh4ifr0s4g4k7r3d057lzyh1jvwnr80gs2jfcw3s"; depends=[BiocParallel BRISC Matrix matrixStats SingleCellExperiment SpatialExperiment SummarizedExperiment]; }; + nnSVG = derive2 { name="nnSVG"; version="1.4.2"; sha256="1vrb5mfgda7mpvbi05ya08krixz494x4yxijh61msnrnz2vb4h5s"; depends=[BiocParallel BRISC Matrix matrixStats SingleCellExperiment SpatialExperiment SummarizedExperiment]; }; nondetects = derive2 { name="nondetects"; version="2.30.0"; sha256="0grz6hky7598kk7mm3amgda5n2bhjmwld0f06zsbcdjpbsr0rchc"; depends=[arm Biobase HTqPCR limma mvtnorm]; }; normalize450K = derive2 { name="normalize450K"; version="1.28.0"; sha256="0im1q0cnmmk347ql41d8apsshxqp357ksnaf063ybw8lgal0fzv2"; depends=[Biobase illuminaio quadprog]; }; normr = derive2 { name="normr"; version="1.26.0"; sha256="1l1xj3yz2xbi2rd28zj4gbjjdca0x0z4s4v2gqdg6zn87yz318dm"; depends=[bamsignals GenomeInfoDb GenomicRanges IRanges qvalue Rcpp rtracklayer]; }; @@ -1926,7 +1929,7 @@ in with self; { rgoslin = derive2 { name="rgoslin"; version="1.4.0"; sha256="1bbac7i1k79livslclc2zlrw2dcnscwknjmbn4w9748hv9i27y6q"; depends=[dplyr Rcpp]; }; rgsepd = derive2 { name="rgsepd"; version="1.32.0"; sha256="0bk5l4fa4zmd69fasvwqy4z41y0q49ja95r5baa8w4261w4x5jkx"; depends=[AnnotationDbi biomaRt DESeq2 GO_db goseq gplots org_Hs_eg_db SummarizedExperiment]; }; rhdf5 = derive2 { name="rhdf5"; version="2.44.0"; sha256="1akbr55lylwp20b2j351h1gcj1sc5y2j2pjjdpz43m6b7mji23a0"; depends=[rhdf5filters Rhdf5lib]; }; - rhdf5client = derive2 { name="rhdf5client"; version="1.22.2"; sha256="1nvkv281vb3k7r80kzvpi86a5rdfnkkshvifa1ls8d6rm511sk04"; depends=[data_table DelayedArray httr rjson]; }; + rhdf5client = derive2 { name="rhdf5client"; version="1.22.3"; sha256="1qhsr4np16fhxn4mzlv1krp41q7y6fwaydf7k0wq34r6gskg2mwz"; depends=[data_table DelayedArray httr rjson]; }; rhdf5filters = derive2 { name="rhdf5filters"; version="1.12.1"; sha256="1v9wxa5q0iwphrmkf9x70jpbq9r9rqz2hm94smqnnpfxszila49m"; depends=[Rhdf5lib]; }; ribor = derive2 { name="ribor"; version="1.12.0"; sha256="0qf6yracvzc1sxa40l24y0wx14dj7rr1s60qxircx5zzq7c3xa5m"; depends=[dplyr ggplot2 hash rhdf5 rlang S4Vectors tidyr yaml]; }; ribosomeProfilingQC = derive2 { name="ribosomeProfilingQC"; version="1.12.0"; sha256="0q1fl1w2ab7hmzgyp8d66nfr0fl7d32gvbh851sr6g2vx7rbnknn"; depends=[AnnotationDbi BiocGenerics Biostrings BSgenome cluster EDASeq GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggfittext ggplot2 ggrepel IRanges motifStack Rsamtools Rsubread rtracklayer RUVSeq S4Vectors scales XVector]; }; @@ -1943,13 +1946,13 @@ in with self; { rpx = derive2 { name="rpx"; version="2.8.0"; sha256="1ay127hn7hq3dhs2sb1ah8d1xvzldnmam8yxbwwhsymxfkhidy9h"; depends=[BiocFileCache curl jsonlite RCurl xml2]; }; rqt = derive2 { name="rqt"; version="1.26.0"; sha256="0by212x06h2k6mcwzam78n4w7f9akl7qbnpdkyiy2dd6jiq89bdv"; depends=[car CompQuadForm glmnet Matrix metap pls ropls RUnit SummarizedExperiment]; }; rqubic = derive2 { name="rqubic"; version="1.46.0"; sha256="0hshaxa19nk43x4nscsbzd8f0pa8138yaxz0lwfywrs2mya5y7jg"; depends=[biclust Biobase BiocGenerics]; }; - rrvgo = derive2 { name="rrvgo"; version="1.12.0"; sha256="0h6w1dncbazda98jam69znn009mv7z660rllvffwg32133rcckcf"; depends=[AnnotationDbi ggplot2 ggrepel GO_db GOSemSim pheatmap shiny tm treemap umap wordcloud]; }; + rrvgo = derive2 { name="rrvgo"; version="1.12.2"; sha256="1400y3mpyhbf0yzkfgj6bq03077da80y6g1gxr7rp3154260dql3"; depends=[AnnotationDbi ggplot2 ggrepel GO_db GOSemSim pheatmap shiny tm treemap umap wordcloud]; }; rsbml = derive2 { name="rsbml"; version="2.58.0"; sha256="0mgg1qfvxgyjk6fw4x0cv486vrsgf1kbqr6nqhgxj6lk8w6909fm"; depends=[BiocGenerics graph]; }; rsemmed = derive2 { name="rsemmed"; version="1.10.0"; sha256="06nbbymllyd7aa203mrip10q24xj249xhzhl3h9r8pdb7c4xh1f5"; depends=[dplyr igraph magrittr stringr]; }; - rtracklayer = derive2 { name="rtracklayer"; version="1.60.0"; sha256="0gy8df0ndq6nyly4b5h3kby8k77rc4j9n7zhnliryvirpr6alm9m"; depends=[BiocGenerics BiocIO Biostrings GenomeInfoDb GenomicAlignments GenomicRanges IRanges RCurl restfulr Rsamtools S4Vectors XML XVector zlibbioc]; }; + rtracklayer = derive2 { name="rtracklayer"; version="1.60.1"; sha256="06z02sz8zjg2lxp2q4qwhvh6dsi6srirdmhcdvmi3as50nnjmzd8"; depends=[BiocGenerics BiocIO Biostrings GenomeInfoDb GenomicAlignments GenomicRanges IRanges RCurl restfulr Rsamtools S4Vectors XML XVector zlibbioc]; }; runibic = derive2 { name="runibic"; version="1.22.0"; sha256="0q67vyny6qsh6slcjpmvmd3i9qh71qf37nx1isb3dc06680708a1"; depends=[biclust Rcpp SummarizedExperiment testthat]; }; sRACIPE = derive2 { name="sRACIPE"; version="1.16.0"; sha256="1318nrm65c5n2n4822nph7l83klrp1iik8jprr7j9qgbbzdlwwjh"; depends=[BiocGenerics ggplot2 gplots gridExtra htmlwidgets MASS RColorBrewer Rcpp reshape2 S4Vectors SummarizedExperiment umap visNetwork]; }; - sSNAPPY = derive2 { name="sSNAPPY"; version="1.4.4"; sha256="0gkps9gr3ql85qz6ijjqa1ls1s8a819s2fhwlji3nfb8c24k0nd1"; depends=[dplyr edgeR ggforce ggplot2 ggraph graphite gtools igraph magrittr org_Hs_eg_db pheatmap reshape2 rlang stringr SummarizedExperiment tibble tidyr]; }; + sSNAPPY = derive2 { name="sSNAPPY"; version="1.4.6"; sha256="1hnm3yhbwc1wl76akcm9r1c1l6k424nicdcp0s9i531lnh7yg5fg"; depends=[dplyr edgeR ggforce ggplot2 ggraph graphite gtools igraph magrittr org_Hs_eg_db pheatmap reshape2 rlang stringr SummarizedExperiment tibble tidyr]; }; sSeq = derive2 { name="sSeq"; version="1.38.0"; sha256="05c0pxw38bgijd39i92jxm3kwm0dihdff83cdh48saj240ynf7sp"; depends=[caTools RColorBrewer]; }; safe = derive2 { name="safe"; version="3.40.1"; sha256="17m49wvqbwxmw0b08vp5s9qsm67x967xm8znb5nj32915cj9diif"; depends=[AnnotationDbi Biobase SparseM]; }; sagenhaft = derive2 { name="sagenhaft"; version="1.70.0"; sha256="02q0y9r098rimqxm6hzbpkdsij0smg55amxy6pyahjh6yn5jcp91"; depends=[SparseM]; }; @@ -2003,7 +2006,7 @@ in with self; { screenCounter = derive2 { name="screenCounter"; version="1.0.1"; sha256="1yl1sypx11f3iz6kfb5z58smwmkpdd1pm9fgkk6dsg7qm4p6j0la"; depends=[BiocParallel Rcpp S4Vectors SummarizedExperiment zlibbioc]; }; scruff = derive2 { name="scruff"; version="1.18.0"; sha256="07mjd3y4kyd8536j9q8m3vxpfb2a92s0hb6wsgcpb2c45fxayg3c"; depends=[AnnotationDbi BiocGenerics BiocParallel Biostrings data_table GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggbio ggplot2 ggthemes plyr Rsamtools Rsubread rtracklayer S4Vectors scales ShortRead SingleCellExperiment stringdist SummarizedExperiment]; }; scry = derive2 { name="scry"; version="1.12.0"; sha256="0406slld468m9lxswv1akcdmap6izvzz6zljyrs5av546nfxpmrz"; depends=[BiocSingular DelayedArray glmpca Matrix SingleCellExperiment SummarizedExperiment]; }; - scuttle = derive2 { name="scuttle"; version="1.10.2"; sha256="0225fk3ca540b9z3dd5q2zngxsa524nq7zrv1z5qnmr2knc0yxfb"; depends=[beachmat BiocGenerics BiocParallel DelayedArray DelayedMatrixStats GenomicRanges Matrix Rcpp S4Vectors SingleCellExperiment SummarizedExperiment]; }; + scuttle = derive2 { name="scuttle"; version="1.10.3"; sha256="0nngajyfix3b4p072aqf2vbk346gpxq326vd3dnqmq4hryww3j9y"; depends=[beachmat BiocGenerics BiocParallel DelayedArray DelayedMatrixStats GenomicRanges Matrix Rcpp S4Vectors SingleCellExperiment SummarizedExperiment]; }; scviR = derive2 { name="scviR"; version="1.0.0"; sha256="04yz41qzgy87frxnykvnsyf1kjaw629fr5hrjv9m4k5jdmqrc0bl"; depends=[basilisk BiocFileCache limma pheatmap reticulate S4Vectors scater shiny SingleCellExperiment SummarizedExperiment]; }; sechm = derive2 { name="sechm"; version="1.8.0"; sha256="1wsf3bhxm48wvyl9g6hhcb1mgy6hds27w6yibyjs695gf4ni5p7p"; depends=[circlize ComplexHeatmap matrixStats randomcoloR S4Vectors seriation SummarizedExperiment]; }; segmenter = derive2 { name="segmenter"; version="1.6.0"; sha256="04sfk7r3qg0jx1aqh7vhnmq5zy0ilg96zbzaqvjfg70bir5v6scd"; depends=[bamsignals ChIPseeker chromhmmData ComplexHeatmap GenomicRanges IRanges S4Vectors SummarizedExperiment]; }; @@ -2024,7 +2027,7 @@ in with self; { sesame = derive2 { name="sesame"; version="1.18.4"; sha256="1il33ygys6y72l8p3fhx301q16w9kylfy6w92b64n8gqkn6dmsmn"; depends=[BiocFileCache BiocParallel dplyr GenomeInfoDb GenomicRanges ggplot2 illuminaio IRanges MASS preprocessCore readr reshape2 S4Vectors sesameData stringr SummarizedExperiment tibble wheatmap]; }; sevenC = derive2 { name="sevenC"; version="1.20.0"; sha256="0mgngw3cvqm25jjsymxwfhykc7riip28c5bvkfkb6xcbakp6bqj6"; depends=[BiocGenerics boot data_table GenomeInfoDb GenomicRanges InteractionSet IRanges purrr readr rtracklayer S4Vectors]; }; sevenbridges = derive2 { name="sevenbridges"; version="1.30.0"; sha256="1sym0sjyn4ppsixmwxg84g669xf7jahmx76xl7qfk0m2zz9r0100"; depends=[curl data_table docopt httr jsonlite objectProperties S4Vectors stringr uuid yaml]; }; - shinyMethyl = derive2 { name="shinyMethyl"; version="1.36.0"; sha256="1rqwwglj0475gr14bxazfmcvsy7rq6nlw2zcswa684751wy15w0r"; depends=[Biobase BiocGenerics htmltools MatrixGenerics minfi RColorBrewer shiny]; }; + shinyMethyl = derive2 { name="shinyMethyl"; version="1.36.1"; sha256="0hq1q66vjd9pwdwm9zx8q45ws65bn6cm87zmjmyc3md8dwvb8cck"; depends=[Biobase BiocGenerics htmltools MatrixGenerics minfi RColorBrewer shiny]; }; shinyepico = derive2 { name="shinyepico"; version="1.8.0"; sha256="0f9zv3ds9l0bisp8lif0g664i0y59ygrlazhbdxkd7v9ypg22qz1"; depends=[data_table doParallel dplyr DT foreach GenomicRanges ggplot2 gplots heatmaply limma minfi plotly reshape2 rlang rmarkdown rtracklayer shiny shinycssloaders shinyjs shinythemes shinyWidgets statmod tidyr zip]; }; sigFeature = derive2 { name="sigFeature"; version="1.18.0"; sha256="00gqfzbymmma6j0a9j6jf2pv4gahjh70a6pyp6kjnzs5zdmsh7z1"; depends=[BiocParallel biocViews e1071 Matrix nlme openxlsx pheatmap RColorBrewer SparseM SummarizedExperiment]; }; siggenes = derive2 { name="siggenes"; version="1.74.0"; sha256="0h5asj2w4xgfj9xapjawmxldnhq789py39drlr8illyhcczkzkbz"; depends=[Biobase multtest scrime]; }; @@ -2034,7 +2037,7 @@ in with self; { signifinder = derive2 { name="signifinder"; version="1.2.1"; sha256="1xsbnk7igq5avg4lh63iwaqrp36cnqxdqmqqz13z7ls3nlgryq7q"; depends=[AnnotationDbi BiocGenerics ComplexHeatmap consensusOV cowplot DGEobj_utils dplyr ensembldb ggplot2 ggridges GSVA IRanges magrittr matrixStats maxstat openair org_Hs_eg_db patchwork RColorBrewer SummarizedExperiment survival survminer TxDb_Hsapiens_UCSC_hg19_knownGene TxDb_Hsapiens_UCSC_hg38_knownGene viridis]; }; sigsquared = derive2 { name="sigsquared"; version="1.32.0"; sha256="1xbza4mccyyby4wlv2fdi5afcqf3g069p83czprlvmfz2rym9vil"; depends=[Biobase survival]; }; similaRpeak = derive2 { name="similaRpeak"; version="1.32.0"; sha256="0sjkzal9wixd421znrlgy6rbczkrqrdykcidm5jn1w48197aczh9"; depends=[R6]; }; - simpleSeg = derive2 { name="simpleSeg"; version="1.2.0"; sha256="1fsp5z46y9br0z0pb7ygn1lns3rk0lml45msq2g1r0rq5vhwm5hw"; depends=[BiocParallel cytomapper EBImage S4Vectors spatstat_geom SummarizedExperiment terra]; }; + simpleSeg = derive2 { name="simpleSeg"; version="1.2.5"; sha256="17hg6nscvk5w3j0ii0qbn2v251nipglxdiq4ry6k5wyi3n92b7qn"; depends=[BiocParallel cytomapper EBImage S4Vectors spatstat_geom SummarizedExperiment terra]; }; simplifyEnrichment = derive2 { name="simplifyEnrichment"; version="1.10.0"; sha256="1vs57j361fbwv7vaybs71vc208qn76djmbmakhwwcvxwrx77jp5f"; depends=[AnnotationDbi BiocGenerics circlize clue cluster colorspace ComplexHeatmap digest GetoptLong GlobalOptions GO_db GOSemSim Matrix org_Hs_eg_db proxyC slam tm]; }; sincell = derive2 { name="sincell"; version="1.32.0"; sha256="09h47w87459k4vhmcjfi1vf47sh1q5qrbrasdg9jsg3cykwhj6vj"; depends=[cluster entropy fastICA fields ggplot2 igraph MASS proxy Rcpp reshape2 Rtsne scatterplot3d statmod TSP]; }; single = derive2 { name="single"; version="1.4.0"; sha256="1khfbcyn0jwl5gcsmxzzzgqvd5hp73qmn8hpjs4rb54grv73jqwy"; depends=[BiocGenerics Biostrings dplyr GenomicAlignments IRanges reshape2 rlang Rsamtools stringr tidyr]; }; @@ -2058,11 +2061,11 @@ in with self; { sparseMatrixStats = derive2 { name="sparseMatrixStats"; version="1.12.2"; sha256="00jalzg6yphi8ci4iid7x38jlsrvvdswrq7cqa7jybs26ayjldw1"; depends=[Matrix MatrixGenerics matrixStats Rcpp]; }; sparsenetgls = derive2 { name="sparsenetgls"; version="1.18.0"; sha256="0gd7as4hsb8nfkqlk1kihwlm55rrdv36xl28zpxz7by6x9w92rjk"; depends=[glmnet huge MASS Matrix]; }; spatialDE = derive2 { name="spatialDE"; version="1.6.0"; sha256="18fgyans15wnc63kzmv51yaxxd3vxjv3q9hgyrk9dz6kqx928mng"; depends=[basilisk checkmate ggplot2 ggrepel gridExtra Matrix reticulate scales SpatialExperiment SummarizedExperiment]; }; - spatialHeatmap = derive2 { name="spatialHeatmap"; version="2.6.0"; sha256="03cpwkz7glfkdlp9967ikgplcj42cw5gyby4w0v41mdyw3y353nk"; depends=[data_table dplyr dynamicTreeCut edgeR flashClust genefilter ggdendro ggplot2 ggplotify gplots gridExtra grImport htmlwidgets igraph Matrix plotly reshape2 rsvg S4Vectors scater scran scuttle shiny shinydashboard SingleCellExperiment SummarizedExperiment tibble UpSetR visNetwork WGCNA xml2 yaml]; }; + spatialHeatmap = derive2 { name="spatialHeatmap"; version="2.6.2"; sha256="10gpil8l3q6pm76509z4jl25i72595yxgrcnkz8zd05dx4jjf8pr"; depends=[data_table dplyr edgeR genefilter ggplot2 ggplotify gplots gridExtra grImport igraph Matrix reshape2 rsvg S4Vectors scater scran scuttle shiny shinydashboard SingleCellExperiment spsComps SummarizedExperiment tibble xml2]; }; spatzie = derive2 { name="spatzie"; version="1.6.0"; sha256="0c460pdfm4ncijhqj47j08bdhgiiic9aha5dwz2bpl1fk4p5l8x1"; depends=[BiocGenerics BSgenome GenomeInfoDb GenomicFeatures GenomicInteractions GenomicRanges ggplot2 IRanges MatrixGenerics matrixStats motifmatchr S4Vectors SummarizedExperiment TFBSTools]; }; specL = derive2 { name="specL"; version="1.34.0"; sha256="00b4iwq43f3jr8a3g1a86wwvka20zm4jb2lwfv140n4qw3fg294k"; depends=[DBI protViz RSQLite seqinr]; }; speckle = derive2 { name="speckle"; version="1.0.0"; sha256="09hf4kb9s6dcv0532q13ikbbknj4x5il0rxgc34d4k3sbf8pph5s"; depends=[edgeR ggplot2 limma Seurat SingleCellExperiment]; }; - spicyR = derive2 { name="spicyR"; version="1.12.0"; sha256="1gnmzynqc1pnpyzb0481313hrq3dw8g6k5ka97shaldr2cv5c553"; depends=[BiocGenerics BiocParallel concaveman data_table dplyr ggforce ggplot2 IRanges lme4 lmerTest mgcv pheatmap rlang S4Vectors scam SingleCellExperiment SpatialExperiment spatstat_explore spatstat_geom SummarizedExperiment tidyr]; }; + spicyR = derive2 { name="spicyR"; version="1.12.2"; sha256="04x8gpl15j63k9qly9fsv0vlz9gki4kix2ncysz226qsxmzqpc0v"; depends=[BiocGenerics BiocParallel ClassifyR concaveman data_table dplyr ggforce ggplot2 IRanges lme4 lmerTest mgcv pheatmap rlang S4Vectors scam SingleCellExperiment SpatialExperiment spatstat_explore spatstat_geom SummarizedExperiment tidyr]; }; spikeLI = derive2 { name="spikeLI"; version="2.60.0"; sha256="0mh24piab0gjcjk4lc3wji19lfx2mk0hch9p3wbqkahag6d4y785"; depends=[]; }; spiky = derive2 { name="spiky"; version="1.6.0"; sha256="1lhv69z52pamzrp1pb9ccngdn4kkija4rb7g4vahp1wx7d5fbbja"; depends=[bamlss Biostrings BlandAltmanLeh BSgenome GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 IRanges Rsamtools S4Vectors scales]; }; spkTools = derive2 { name="spkTools"; version="1.56.0"; sha256="14rqm15ym7vnzzqk2r4sa7fwa4a474y4i1jxzdy66aarf8nck57j"; depends=[Biobase gtools RColorBrewer]; }; @@ -2084,7 +2087,7 @@ in with self; { stepNorm = derive2 { name="stepNorm"; version="1.72.0"; sha256="1j915bnmq1fsjdgn0rrlxmqvmy1cafyp5sc2gal81qrv366qy1ri"; depends=[marray MASS]; }; strandCheckR = derive2 { name="strandCheckR"; version="1.18.0"; sha256="0gsnhx7vfi3p665fwyai8byz984j7ai6k8d7ilbpxi5f3v1qkjrk"; depends=[BiocGenerics dplyr GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 gridExtra IRanges magrittr reshape2 rmarkdown Rsamtools S4Vectors stringr TxDb_Hsapiens_UCSC_hg38_knownGene]; }; struct = derive2 { name="struct"; version="1.12.0"; sha256="1vf92g3lhq3ciy6sr9vwx4xzqpzf28np1nfc2f63d5dwcq24l8a9"; depends=[knitr ontologyIndex rols S4Vectors SummarizedExperiment]; }; - structToolbox = derive2 { name="structToolbox"; version="1.12.2"; sha256="1knasb5rna4mgwzwsyxa17v85753769l48jpyvfr3jsysfqv2q0h"; depends=[ggplot2 ggthemes gridExtra scales sp struct]; }; + structToolbox = derive2 { name="structToolbox"; version="1.12.3"; sha256="0g0glzijv4vrpics14fpj2gs5f8la2rg6n5a71jyh0dzyycj87b5"; depends=[ggplot2 ggthemes gridExtra scales sp struct]; }; subSeq = derive2 { name="subSeq"; version="1.30.0"; sha256="1p035a53129ax84cjyv1xx3gcq4940mr4ppakczqdbc8c3ch4d08"; depends=[Biobase data_table digest dplyr ggplot2 magrittr qvalue tidyr]; }; supersigs = derive2 { name="supersigs"; version="1.8.0"; sha256="0ifj0558rcf3v6rwpl2i0bidbg1gv3q8calpn49s1jqayn57hiik"; depends=[assertthat Biostrings caret dplyr rlang rsample SummarizedExperiment tidyr]; }; supraHex = derive2 { name="supraHex"; version="1.38.0"; sha256="1z216mrm59sgxf7kspscf26ic3qlrvpwjs013z10vsxrjwypkmw7"; depends=[ape dplyr hexbin igraph magrittr MASS purrr readr stringr tibble tidyr]; }; @@ -2141,7 +2144,7 @@ in with self; { traviz = derive2 { name="traviz"; version="1.6.0"; sha256="1lsczylj86w2cq2hcknswzqdp4b298gcv6ljzdr9c8ir7ks2j55k"; depends=[Biobase ggplot2 mgcv princurve RColorBrewer rgl SingleCellExperiment slingshot SummarizedExperiment viridis]; }; treeio = derive2 { name="treeio"; version="1.24.3"; sha256="0shm0mdqvsk5qipdqbz3251kks6ii1vpx1pph0ms271nzs6fcvif"; depends=[ape cli dplyr jsonlite magrittr rlang tibble tidytree]; }; treekoR = derive2 { name="treekoR"; version="1.8.0"; sha256="1gsvs30n67vf3fqbm0d6zg5dxj2m1bi81gnm8vjg39413cqi63pc"; depends=[ape data_table diffcyt dplyr edgeR ggiraph ggplot2 ggtree hopach lme4 multcomp patchwork SingleCellExperiment tidyr]; }; - trena = derive2 { name="trena"; version="1.21.0"; sha256="04i4vjdcamjbw3mslnqk3ra2fk3432p9rj376chqapkj9anfpm82"; depends=[AnnotationDbi biomaRt Biostrings BSgenome BSgenome_Hsapiens_UCSC_hg19 BSgenome_Hsapiens_UCSC_hg38 BSgenome_Mmusculus_UCSC_mm10 DBI GenomicRanges glmnet lassopv MotifDb org_Hs_eg_db randomForest RMySQL RPostgreSQL RSQLite SNPlocs_Hsapiens_dbSNP150_GRCh38 WGCNA xgboost]; }; + trena = derive2 { name="trena"; version="1.22.2"; sha256="1xjhqm2g53kgcnnqhs5l3vn525h7amaz4hvsskjp5zb0gkfpiwh1"; depends=[AnnotationDbi biomaRt Biostrings BSgenome BSgenome_Hsapiens_UCSC_hg19 BSgenome_Hsapiens_UCSC_hg38 BSgenome_Mmusculus_UCSC_mm10 DBI GenomicRanges glmnet lassopv MotifDb org_Hs_eg_db randomForest RMySQL RPostgreSQL RSQLite SNPlocs_Hsapiens_dbSNP150_GRCh38 WGCNA xgboost]; }; tricycle = derive2 { name="tricycle"; version="1.8.0"; sha256="1ags05rhi431jsk0kqs7rmxj853mf5c0ibfqknbwy2wmbz8p1vq6"; depends=[AnnotationDbi circular dplyr GenomicRanges ggnewscale ggplot2 IRanges RColorBrewer S4Vectors scater scattermore SingleCellExperiment SummarizedExperiment]; }; trigger = derive2 { name="trigger"; version="1.46.0"; sha256="0wviwgr1f8549rwg4hd80c1jri79fqwiylgkablx8h7izq5lk1fc"; depends=[corpcor qtl qvalue sva]; }; trio = derive2 { name="trio"; version="3.38.0"; sha256="1jzsdwpc4wqvdqmqai7lc0hyvl7rq32442iihfhx31yhr78gqn1g"; depends=[LogicReg siggenes survival]; }; @@ -2153,7 +2156,7 @@ in with self; { twilight = derive2 { name="twilight"; version="1.76.0"; sha256="0xhwykvb9rgsj13ivfjlal4ffhms9sglh9h61h8448r9g58kgibz"; depends=[Biobase]; }; twoddpcr = derive2 { name="twoddpcr"; version="1.24.0"; sha256="0klikcpvpd7dm6ssyv08vd1iv5hhas5a2b7wjkapn2p2j43b214n"; depends=[class ggplot2 hexbin RColorBrewer S4Vectors scales shiny]; }; txcutr = derive2 { name="txcutr"; version="1.6.0"; sha256="1xbpyvcs1r7z5h0khl3avz3rnc8422fsyqvfpiwhy45icqwvlpbq"; depends=[AnnotationDbi BiocGenerics BiocParallel Biostrings GenomicFeatures GenomicRanges IRanges rtracklayer S4Vectors]; }; - tximeta = derive2 { name="tximeta"; version="1.18.1"; sha256="02240v41scaqxabjb62zh6shkkzb9520dhn0lfc2jbimnb26yj7f"; depends=[AnnotationDbi AnnotationHub BiocFileCache Biostrings ensembldb GenomeInfoDb GenomicFeatures GenomicRanges IRanges jsonlite Matrix S4Vectors SummarizedExperiment tibble tximport]; }; + tximeta = derive2 { name="tximeta"; version="1.18.3"; sha256="01s8x8a3rb0a5i599pxc5miz84ssvh10b4vha79nmbhkqccffvml"; depends=[AnnotationDbi AnnotationHub BiocFileCache Biostrings ensembldb GenomeInfoDb GenomicFeatures GenomicRanges IRanges jsonlite Matrix S4Vectors SummarizedExperiment tibble tximport]; }; tximport = derive2 { name="tximport"; version="1.28.0"; sha256="0km1vfn4jcp05jk5srrqanjngq6ghh5im6h1c424b926g9s7w7k1"; depends=[]; }; uSORT = derive2 { name="uSORT"; version="1.26.0"; sha256="0mqf481niq5md6ld0mki4iif4vhpnjk57896vaqvjzwjdhnw8n2b"; depends=[Biobase BiocGenerics cluster fpc gplots igraph Matrix monocle plyr RANN RSpectra VGAM]; }; uncoverappLib = derive2 { name="uncoverappLib"; version="1.10.0"; sha256="063iblr2mal7wsci52zhd51hpjmxm5jbz08f3i2yxc6z72qi97nd"; 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]; }; @@ -2217,7 +2220,6 @@ in with self; { GRridge = derive2 { name="GRridge"; version="1.22.0"; sha256="0vmwm50dwk3im3qx40vh9ipmfqywzz5fmmm79b74zjcd3qjrznf3"; depends=[glmnet graph Iso mvtnorm penalized survival]; broken = true; }; GeneAccord = derive2 { name="GeneAccord"; version="1.15.0"; sha256="1dlnqdcrl1fv5yf0zwfgkqfd2x19fv6q84p7c730nmnnaqal6md1"; depends=[biomaRt caTools dplyr ggplot2 ggpubr gtools magrittr maxLik RColorBrewer reshape2 tibble]; broken = true; }; GeneAnswers = derive2 { name="GeneAnswers"; version="2.36.0"; sha256="1f8q3hi913khyy1cc3yp2635gaik47alsqmhi0mi24cy340faplz"; depends=[annotate Biobase downloader Heatplus igraph KEGGREST MASS RBGL RColorBrewer RCurl RSQLite XML]; broken = true; }; - GeneGA = derive2 { name="GeneGA"; version="1.48.0"; sha256="136z3sxjps1k63ivr0cmqg7xkvbzf7j69vwkfbc1n00yfapiprm2"; depends=[hash seqinr]; broken = true; }; GenoGAM = derive2 { name="GenoGAM"; version="2.11.0"; sha256="058qix2h0zm2k9csmbdhci2wqih3lyggjj591cqn0ls2nv7bnyvj"; depends=[BiocParallel Biostrings data_table DelayedArray DESeq2 futile_logger GenomeInfoDb GenomicAlignments GenomicRanges HDF5Array IRanges Matrix Rcpp RcppArmadillo rhdf5 Rsamtools S4Vectors sparseinv SummarizedExperiment]; broken = true; }; IsoGeneGUI = derive2 { name="IsoGeneGUI"; version="2.31.0"; sha256="1w7zxsvmcrz8cj8g8xa1vqbzfycdhgsclhcjmkqjw1hwz6fp3xgn"; depends=[Biobase ff geneplotter goric Iso IsoGene jpeg multtest ORCME ORIClust RColorBrewer Rcpp relimp tkrplot xlsx]; broken = true; }; LowMACA = derive2 { name="LowMACA"; version="1.28.0"; sha256="0j5233xziszwak65rypd9f8lsp25sdr4j5nm5kanj4d4wd0zsdqv"; depends=[BiocParallel Biostrings cBioPortalData data_table gridBase httr LowMACAAnnotation motifStack plyr RColorBrewer reshape2 stringr]; broken = true; }; @@ -2229,7 +2231,6 @@ in with self; { MSstatsTMTPTM = derive2 { name="MSstatsTMTPTM"; version="1.1.2"; sha256="16qnddwhwhjjfr5akdrmp93gkxq2r41s82hb1blbz47lwbj5kaj5"; depends=[dplyr ggplot2 gridExtra MSstatsTMT Rcpp reshape2 stringr]; broken = true; }; MethCP = derive2 { name="MethCP"; version="1.11.0"; sha256="099jaadjfalvxpwq3k630yrqa1dfbp8rqn2fahz1rsha3y5z9bys"; depends=[BiocParallel bsseq DNAcopy DSS GenomeInfoDb GenomicRanges IRanges methylKit S4Vectors]; broken = true; }; NBSplice = derive2 { name="NBSplice"; version="1.15.0"; sha256="0yn7s7igshall34cflmdwvmknv8h1zdi6vg8svvcyn9fvzlgjdm8"; depends=[BiocParallel car edgeR ggplot2 MASS reshape2]; broken = true; }; - NewWave = derive2 { name="NewWave"; version="1.8.0"; sha256="13zwn5qzh9mjhp6d72yndymwbmi4hb7s8qg6ji0nmqp53gj30lc8"; depends=[BiocSingular DelayedArray irlba Matrix SharedObject SingleCellExperiment SummarizedExperiment]; broken = true; }; PSICQUIC = derive2 { name="PSICQUIC"; version="1.34.0"; sha256="0gkkxxbc2a7cin92qwn1masqfigyz9s4fhyy2daa17r3ckk4ccgx"; depends=[BiocGenerics biomaRt httr IRanges plyr RCurl]; broken = true; }; PanVizGenerator = derive2 { name="PanVizGenerator"; version="1.22.0"; sha256="0rhx2jc5kc9bl00v16frh8b4075n0jqn4s37pkvqp3ypcbqws32d"; depends=[igraph jsonlite pcaMethods shiny]; broken = true; }; PoTRA = derive2 { name="PoTRA"; version="1.13.0"; sha256="1a32d1wndb24pxza3h53yddj9z2clff5srny2k00pbbfq1h99mjf"; depends=[BiocGenerics graph graphite igraph org_Hs_eg_db]; broken = true; }; @@ -2245,7 +2246,6 @@ in with self; { SLGI = derive2 { name="SLGI"; version="1.54.0"; sha256="03jwdq4k44rys3f773c6l985a6v1bacbdghw97p0qpwspmzra8rs"; depends=[AnnotationDbi Biobase BiocGenerics GO_db lattice]; broken = true; }; STAN = derive2 { name="STAN"; version="2.26.2"; sha256="0dd4hb2iabvnr6v0ys4jslj7611z1hii8hxkdvwrjbz4nn678wkv"; depends=[BiocGenerics GenomeInfoDb GenomicRanges Gviz IRanges poilog Rsolnp S4Vectors]; broken = true; }; ScISI = derive2 { name="ScISI"; version="1.65.0"; sha256="0q3bbfsink5d8xslhp129qwvlq5mdzw8zkv9msd0q8qmkclsbiz1"; depends=[annotate AnnotationDbi apComplex GO_db org_Sc_sgd_db RpsiXML]; broken = true; }; - SharedObject = derive2 { name="SharedObject"; version="1.12.0"; sha256="11rrnm7kjm6z8j4ga88s4cafcdj83pvhnybp7ns5pn7s2ln8044d"; depends=[BH BiocGenerics Rcpp]; broken = true; }; Sushi = derive2 { name="Sushi"; version="1.34.0"; sha256="0adswrbzd93rhy3q56ypwkrk6155vd4zxapvznswyjlxp8ha813q"; depends=[biomaRt zoo]; broken = true; }; SwimR = derive2 { name="SwimR"; version="1.29.0"; sha256="0n58x3i4k3icvhg8z60zlhpszv8bb9pain07nl9rszyvmpi71vg2"; depends=[gplots R2HTML signal]; broken = true; }; TCC = derive2 { name="TCC"; version="1.38.0"; sha256="17kkn8xfkf7g8y51nnzsrgn8v65qlh8a4jysn03phk7pnfrmj7jl"; depends=[baySeq DESeq2 edgeR ROC]; broken = true; }; |