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rPackages: CRAN and BioC update

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Justin Bedo 2024-06-17 22:16:55 +10:00
parent ac5698f23c
commit ffe8f85e7b
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4 changed files with 812 additions and 680 deletions
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2
pkgs/development/r-modules/bioc-annotation-packages.nix generated
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@ -7,7 +7,7 @@
let derive2 = derive { biocVersion = "3.19"; };
in with self; {
AHCytoBands = derive2 { name="AHCytoBands"; version="0.99.1"; sha256="0svxxhj3mh5gqik45ikcxnlhnma8n1c0rv8pycj2034cb9ms1dbv"; depends=[]; };
AHEnsDbs = derive2 { name="AHEnsDbs"; version="1.3.1"; sha256="18v0cn80b09g5661an8yhd2rq7ln6gk0w7gsixq8kgnngshndjng"; depends=[AnnotationHubData ensembldb]; };
AHEnsDbs = derive2 { name="AHEnsDbs"; version="1.5.1"; sha256="02gvrlfld6y03gcw7931fplm220dhnhh12xljb0xm6f3inl0vwa6"; depends=[AnnotationHubData ensembldb]; };
AHLRBaseDbs = derive2 { name="AHLRBaseDbs"; version="1.8.0"; sha256="038i0338zyqzkvmhxcdiykb0rwa3bzi0vv18j643b1a64bsnvcxi"; depends=[AnnotationHub]; };
AHMeSHDbs = derive2 { name="AHMeSHDbs"; version="1.8.0"; sha256="09acd6xipzillw9z68nqqxjxa0hbshclv504na7l2dkhpppx6934"; depends=[AnnotationHub]; };
AHPathbankDbs = derive2 { name="AHPathbankDbs"; version="0.99.5"; sha256="10wcrglm521xcrfbzc39dkbjvg1pkz0zq70vgnh68akiwmdirp89"; depends=[AnnotationHub]; };

6
pkgs/development/r-modules/bioc-experiment-packages.nix generated
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@ -311,7 +311,7 @@ in with self; {
gageData = derive2 { name="gageData"; version="2.42.0"; sha256="1kbs0fz1jnx3grd9mpclbahwbp3749ipwfs8ggl9299bhjrgh9i6"; depends=[]; };
gaschYHS = derive2 { name="gaschYHS"; version="1.42.0"; sha256="01r25gx65a9lcjzbjm6gckzy3hyr70cxswxkvprsbphh7pkll3np"; depends=[Biobase]; };
gcspikelite = derive2 { name="gcspikelite"; version="1.42.0"; sha256="0cphbkq13jknmzs6qyv3cj1m73a1wncnj7znjnymbc0ha7rwcd5i"; depends=[]; };
geneLenDataBase = derive2 { name="geneLenDataBase"; version="1.39.0"; sha256="0rdd5nq34xd85r4i4b84ibih31mq99ljvgkm7zdv4gfggrdvi6gb"; depends=[GenomicFeatures rtracklayer]; };
geneLenDataBase = derive2 { name="geneLenDataBase"; version="1.40.1"; sha256="0c8f0sqgrg7rc2vs9id9xzbwwv3zhy6ylqiisji20rw9ipzgv7k8"; depends=[GenomicFeatures rtracklayer txdbmaker]; };
genomationData = derive2 { name="genomationData"; version="1.36.0"; sha256="16mghhik2xzin14d7mqlwfy2dah3ccnga947z9id44vyz906wws7"; depends=[]; };
golubEsets = derive2 { name="golubEsets"; version="1.46.0"; sha256="1rv5y7cj4rpdg8vl0qd3071d12rvgqcffqsf1gx8kmdgz13hi4gl"; depends=[Biobase]; };
gpaExample = derive2 { name="gpaExample"; version="1.16.0"; sha256="0q87x5k8ql01k9m503k87wn5pkrygrilqrsb0aix7xjpxa8aia1n"; depends=[]; };
@ -413,7 +413,7 @@ in with self; {
simpIntLists = derive2 { name="simpIntLists"; version="1.40.0"; sha256="03d7whna1h2ffgci060gqfdwbjwmjg6q3yfd8l6vc25kiblc4igp"; depends=[]; };
smokingMouse = derive2 { name="smokingMouse"; version="1.2.0"; sha256="1z3kbmlqylmaingkcdm6wxlx848zipqfh6kha7f55s6aklgcv5d7"; depends=[]; };
spatialDmelxsim = derive2 { name="spatialDmelxsim"; version="1.10.0"; sha256="172hgg2wxjc32950lga8fqwygd6x07i0ilsvfp46sd7nmysy6cpn"; depends=[ExperimentHub SummarizedExperiment]; };
spatialLIBD = derive2 { name="spatialLIBD"; version="1.16.0"; sha256="0c2r922iw206z952wfq10gj00gjksar22ncsafjhr2x0dmrqvlww"; depends=[AnnotationHub benchmarkme BiocFileCache BiocGenerics cowplot DT edgeR ExperimentHub fields GenomicRanges ggplot2 golem IRanges jsonlite limma magick Matrix MatrixGenerics paletteer plotly png RColorBrewer rlang rtracklayer S4Vectors scater scuttle sessioninfo shiny shinyWidgets SingleCellExperiment SpatialExperiment statmod SummarizedExperiment tibble viridisLite]; };
spatialLIBD = derive2 { name="spatialLIBD"; version="1.16.2"; sha256="0bbwh9mfz7iscv8a1jlc7g1c452hv4qr95hwv3z6h2mqf8pcr5g8"; depends=[AnnotationHub benchmarkme BiocFileCache BiocGenerics cowplot DT edgeR ExperimentHub fields GenomicRanges ggplot2 golem IRanges jsonlite limma magick Matrix MatrixGenerics paletteer plotly png RColorBrewer rlang rtracklayer S4Vectors scater scuttle sessioninfo shiny shinyWidgets SingleCellExperiment SpatialExperiment statmod SummarizedExperiment tibble viridisLite]; };
spqnData = derive2 { name="spqnData"; version="1.16.0"; sha256="047dbhcfqs0zddmnfpabpjhym86m5zlxnwccidkx0b131wxb22gv"; depends=[SummarizedExperiment]; };
stemHypoxia = derive2 { name="stemHypoxia"; version="1.40.0"; sha256="0i8rvz2l6hgzd4zcmfzszjck0riy2m34qf2nidrxx6bjza4iqwpy"; depends=[]; };
synapterdata = derive2 { name="synapterdata"; version="1.42.0"; sha256="0p6rrnqvdifrajil2akjvrzjm1k7gyywspg5cb5p2k62lyz0f06k"; depends=[synapter]; };
@ -435,7 +435,7 @@ in with self; {
yeastGSData = derive2 { name="yeastGSData"; version="0.42.0"; sha256="1m3hrjmibmp8zzcc6acg6m21zq83rpnclya4ivivj60nw6ardbkr"; depends=[]; };
yeastNagalakshmi = derive2 { name="yeastNagalakshmi"; version="1.40.0"; sha256="16n48lcyl63cmlc796xizf19rmm5qmdic0msaadz12wh743phh3a"; depends=[]; };
yeastRNASeq = derive2 { name="yeastRNASeq"; version="0.42.0"; sha256="1jk6451ypys3xskmlm6xpvjxxzrx1g0hnzfcsahf3gqgg63pfj7h"; depends=[]; };
zebrafishRNASeq = derive2 { name="zebrafishRNASeq"; version="1.24.0"; sha256="1d1ix8cmjhimrl2zmykndzhp4dpyr4nashckzs3kf53cflq8bcip"; depends=[]; };
zebrafishRNASeq = derive2 { name="zebrafishRNASeq"; version="1.24.1"; sha256="0khmilw21jnq2ivl7bh7fwz9nxlphljl5fh4w28q9gzydrv0vxci"; depends=[]; };
ABAData = derive2 { name="ABAData"; version="1.24.0"; sha256="1wgniq7ibvjj6dx63ixr3i5yclqmg94qpifzfbzzn9yjj3wnikzr"; depends=[]; broken = true; };
ChIC_data = derive2 { name="ChIC.data"; version="1.22.0"; sha256="1akqpqw9ydf23whr346psciyyp9c3r0rsas1rkdkf8g5wrcj9vhk"; depends=[caret genomeIntervals randomForest]; broken = true; };
DREAM4 = derive2 { name="DREAM4"; version="1.31.0"; sha256="11ypc84agvq0q0v7bk0b25cm48awxay5hhhjd95gw9s7jk196i2p"; depends=[SummarizedExperiment]; broken = true; };

84
pkgs/development/r-modules/bioc-packages.nix generated
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@ -28,7 +28,7 @@ in with self; {
ASAFE = derive2 { name="ASAFE"; version="1.30.0"; sha256="13qf4jvf0m6i46bwqxdhd4zllac370ckwnd9xh6p56r1lrgcl4sa"; depends=[]; };
ASEB = derive2 { name="ASEB"; version="1.48.0"; sha256="1h5rgy2n7rxd72ypzwnfclw8h5hvdnac48fgbfll669z2k97dsmm"; depends=[]; };
ASGSCA = derive2 { name="ASGSCA"; version="1.38.0"; sha256="0gvpb1pspm7zlllg77fbi3g6csa3cpp2lbljna2m0xfi0c5zdqvw"; depends=[MASS Matrix]; };
ASICS = derive2 { name="ASICS"; version="2.20.0"; sha256="1lqw7xmbihx9k9nm43pix0gha4j58brm0wzqf6jmag7zrgc9i6q4"; depends=[BiocParallel ggplot2 glmnet gridExtra Matrix mvtnorm PepsNMR plyr quadprog ropls SummarizedExperiment zoo]; };
ASICS = derive2 { name="ASICS"; version="2.20.1"; sha256="0halznbl3bflnn38rh9h5a5f0dsc88n6x6kwdffbpnin9i192q1k"; depends=[BiocParallel ggplot2 glmnet gridExtra Matrix mvtnorm PepsNMR plyr quadprog ropls SummarizedExperiment zoo]; };
ASSET = derive2 { name="ASSET"; version="2.22.0"; sha256="1wqsnp7w3ml7azrx72fafcfbmjg4324jaxcijpcrlrrccxl5rwp4"; depends=[MASS msm rmeta]; };
ASSIGN = derive2 { name="ASSIGN"; version="1.40.0"; sha256="1aq302awy940jrc1hnsf0rn05y4fg5m9aljsl1mclxxig6b8mrd2"; depends=[ggplot2 gplots msm Rlab sva yaml]; };
ASURAT = derive2 { name="ASURAT"; version="1.8.0"; sha256="1fjzmvc4if1kqhwzhd38l5ryvk2qg3001jwapbnkfagxkhmnwymg"; depends=[circlize cluster ComplexHeatmap plot3D Rcpp S4Vectors SingleCellExperiment SummarizedExperiment]; };
@ -127,7 +127,7 @@ in with self; {
BiocStyle = derive2 { name="BiocStyle"; version="2.32.0"; sha256="1vm9wj4hzzjivdi6rnxyhxwqscdvbmc45w9zq17h3r53qnva530x"; depends=[BiocManager bookdown knitr rmarkdown yaml]; };
BiocVersion = derive2 { name="BiocVersion"; version="3.19.1"; sha256="1zhm28313gsbscfhfdbqizvb5v67n4l0dapjmb1xq010ikly95mh"; depends=[]; };
BiocWorkflowTools = derive2 { name="BiocWorkflowTools"; version="1.30.0"; sha256="1gw0lmdhkzp5ar54yv9jagqmpxp7j9ajfmdqb2y2qrnhh39hymzs"; depends=[BiocStyle bookdown git2r httr knitr rmarkdown rstudioapi stringr usethis]; };
Biostrings = derive2 { name="Biostrings"; version="2.72.0"; sha256="06vh7xa6lsw7y3b3z9s5266s00balr4si3l68hh15dwcsg3md6mh"; depends=[BiocGenerics crayon GenomeInfoDb IRanges S4Vectors XVector]; };
Biostrings = derive2 { name="Biostrings"; version="2.72.1"; sha256="067vy2v7spbdsknvi0fcpdi085kn8v20pyrhkc7wy357v21h7hgs"; depends=[BiocGenerics crayon GenomeInfoDb IRanges S4Vectors XVector]; };
BloodGen3Module = derive2 { name="BloodGen3Module"; version="1.12.0"; sha256="0mksc9jfzcj255a01hg8gjrs6k2plkpfqgv951csldvy7vqrdkma"; depends=[circlize ComplexHeatmap ExperimentHub ggplot2 gtools limma matrixStats preprocessCore randomcoloR reshape2 SummarizedExperiment testthat V8]; };
BridgeDbR = derive2 { name="BridgeDbR"; version="2.14.0"; sha256="0nsn1i5ah3l95wd1afcppxb364l44r3apma0aa79g4jday4zhbv5"; depends=[curl rJava]; };
BrowserViz = derive2 { name="BrowserViz"; version="2.26.0"; sha256="0wq1vc6m54kb8dw6c0qzw8hvvwjq78lqd18whph2nmywjcy9j9hw"; depends=[BiocGenerics httpuv jsonlite]; };
@ -178,7 +178,7 @@ in with self; {
CONFESS = derive2 { name="CONFESS"; version="1.32.0"; sha256="14m7nz6ls58g4c45x5m7r30ms3kgxslg22jikjsi1cx49ycyk9dl"; depends=[changepoint cluster contrast data_table EBImage ecp flexmix flowClust flowCore flowMeans flowMerge flowPeaks foreach ggplot2 limma MASS moments outliers plotrix raster readbitmap reshape2 SamSPECTRAL waveslim wavethresh zoo]; };
CONSTANd = derive2 { name="CONSTANd"; version="1.12.0"; sha256="17vfhh6w2sxnliv68wraf24z85dw369cs58nsrql6xgrm1wyp6h6"; depends=[]; };
COSNet = derive2 { name="COSNet"; version="1.38.0"; sha256="0bb5lz4yqhhq2qjx7381877bwyrmh8286m9yq3fhyhzm4g6l4hfn"; depends=[]; };
COTAN = derive2 { name="COTAN"; version="2.4.1"; sha256="0fis09ahsah659gj9jaj2wqrpagkin6i8q51g93cmz1dlslrm80x"; depends=[assertthat BiocSingular circlize ComplexHeatmap dendextend dplyr ggplot2 ggrepel ggthemes Matrix parallelDist parallelly PCAtools plyr RColorBrewer Rfast rlang scales Seurat stringr tibble tidyr umap withr zeallot]; };
COTAN = derive2 { name="COTAN"; version="2.4.3"; sha256="13yw1mrx38im9g87is0ska6piw0ibzfmkk1h46alj1hxc0n3n5gh"; depends=[assertthat BiocSingular circlize ComplexHeatmap dendextend dplyr ggplot2 ggrepel ggthemes Matrix parallelDist parallelly PCAtools plyr RColorBrewer Rfast rlang scales Seurat stringr tibble tidyr umap withr zeallot]; };
CRISPRball = derive2 { name="CRISPRball"; version="1.0.0"; sha256="1gxwmasr37azvc7h98izv0npxq5n7hvk1bvl2rgj5fv6da2ddmki"; depends=[circlize colourpicker ComplexHeatmap dittoSeq DT ggplot2 htmlwidgets InteractiveComplexHeatmap MAGeCKFlute matrixStats PCAtools plotly shiny shinyBS shinycssloaders shinyjqui shinyjs shinyWidgets]; };
CRISPRseek = derive2 { name="CRISPRseek"; version="1.44.0"; sha256="1vmqwpbl1gplrr45bqs90np0cmrkqshw660k4sxmj9s9k0xdms7c"; depends=[BiocGenerics Biostrings BSgenome data_table DelayedArray dplyr GenomeInfoDb GenomicRanges hash IRanges keras mltools reticulate rhdf5 S4Vectors seqinr XVector]; };
CRImage = derive2 { name="CRImage"; version="1.52.0"; sha256="0nnyzgdn25s2m9x4xglp12z2b4fai5sbfnx935qadk0b9gb62bdg"; depends=[aCGH DNAcopy e1071 EBImage foreach MASS sgeostat]; };
@ -190,7 +190,7 @@ in with self; {
CTexploreR = derive2 { name="CTexploreR"; version="1.0.0"; sha256="0ld0hzd7vynwvks0bjggc3kfgdzb0jlsjxn1ggk68f2gxrqxv8i8"; depends=[BiocGenerics circlize ComplexHeatmap CTdata dplyr GenomicRanges ggplot2 ggrepel IRanges MatrixGenerics rlang SingleCellExperiment SummarizedExperiment tibble tidyr]; };
CaDrA = derive2 { name="CaDrA"; version="1.2.0"; sha256="1m7ggdji6j64b6mz6ak2y8f8xyyi8l1gig5b13ksz7j6fgcbyx71"; depends=[doParallel ggplot2 gplots gtable MASS misc3d plyr ppcor R_cache reshape2 SummarizedExperiment]; };
CaMutQC = derive2 { name="CaMutQC"; version="1.0.0"; sha256="1rri2730mpmz0nqb26kqfq950sgw0x97j8xk9vw09m7g89973zzs"; depends=[clusterProfiler data_table dplyr DT ggplot2 maftools MesKit org_Hs_eg_db stringr tidyr vcfR]; };
Cardinal = derive2 { name="Cardinal"; version="3.6.1"; sha256="1g38x8acpv5nlqzfn5g0h77pmn3426i6y0n8sa14hbkj16xjkagc"; depends=[Biobase BiocGenerics BiocParallel CardinalIO EBImage irlba Matrix matter nlme ProtGenerics S4Vectors]; };
Cardinal = derive2 { name="Cardinal"; version="3.6.2"; sha256="038dlgr4p1x42hb5xrz8apvdi4d18si2vr3r8g3i4aiyvpc2rfwj"; depends=[Biobase BiocGenerics BiocParallel CardinalIO EBImage irlba Matrix matter nlme ProtGenerics S4Vectors]; };
CardinalIO = derive2 { name="CardinalIO"; version="1.2.1"; sha256="1kzqz2zba8i5z1pkwwi0hzb6fm7xh22bymkk1jwicyrk94fzfw1l"; depends=[matter ontologyIndex S4Vectors]; };
Category = derive2 { name="Category"; version="2.70.0"; sha256="0paz6h8rsbqvlxxj4di8cl76aybgjr842z5gdv8xi6c2d7zwbclw"; depends=[annotate AnnotationDbi Biobase BiocGenerics DBI genefilter graph GSEABase Matrix RBGL]; };
CausalR = derive2 { name="CausalR"; version="1.36.0"; sha256="0rf37qjl80wczgmb8lbnvzyq10v1fkqdgll24cg4b3vfhsscw0fl"; depends=[igraph]; };
@ -204,6 +204,7 @@ in with self; {
CellTrails = derive2 { name="CellTrails"; version="1.22.0"; sha256="0pqazyf5da9zw95gpmhlj9mbhvv78c0rl6cncy3pij293xcy02l4"; depends=[Biobase BiocGenerics cba dendextend dtw EnvStats ggplot2 ggrepel igraph maptree mgcv reshape2 Rtsne SingleCellExperiment SummarizedExperiment]; };
CelliD = derive2 { name="CelliD"; version="1.12.0"; sha256="0c7hls5qasjd5ahrqxp2mpd402jc12pi0pgy7spcbp1fkqm8qvbl"; depends=[BiocParallel data_table fastmatch fgsea ggplot2 glue irlba Matrix matrixStats pbapply Rcpp RcppArmadillo reticulate Rtsne scater Seurat SingleCellExperiment stringr SummarizedExperiment tictoc umap]; };
CexoR = derive2 { name="CexoR"; version="1.42.0"; sha256="09376wzlknf8nlq81rrbbfsbbgd4mi5aagry51nykw5vc0870vdn"; depends=[genomation GenomeInfoDb GenomicRanges idr IRanges RColorBrewer Rsamtools rtracklayer S4Vectors]; };
ChAMP = derive2 { name="ChAMP"; version="2.34.0"; sha256="06q539yhbmbp7qr71cwjai2vdw5nnhhjdv2ajlqmlyjpg04arc7v"; 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]; };
ChIPComp = derive2 { name="ChIPComp"; version="1.34.0"; sha256="013lmgdkj596gqzm0nlxjqpv0w94hap9vndp5znqpk4inq88gj8m"; depends=[BiocGenerics BSgenome_Hsapiens_UCSC_hg19 BSgenome_Mmusculus_UCSC_mm9 GenomeInfoDb GenomicRanges IRanges limma Rsamtools rtracklayer S4Vectors]; };
ChIPQC = derive2 { name="ChIPQC"; version="1.40.0"; sha256="0lnk5lchwjnrr03x2r6lwgrja42n0rhfp5w9sya2y69da47bcks4"; 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="1.48.0"; sha256="09lkm6s98ip9pw9cwdx8a0z816krr4cgzrcrd7b3d4v4bcywsy7z"; depends=[affy biganalytics bigmemory Biobase ChIPXpressData frma GEOquery]; };
@ -220,7 +221,7 @@ in with self; {
ChromSCape = derive2 { name="ChromSCape"; version="1.14.0"; sha256="12chaigwnqm765p0qlf00s94kkg3dphj2cbqv3vfsyya54hbhfzr"; 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="1.6.0"; sha256="1i9izbf9mzlc7sl2zi5gj4dhxa6mq9kkyysxdq9cj4myhrp9hgwz"; depends=[BiocGenerics Biostrings dplyr ggplot2 htmltools IRanges magrittr plotly R_utils Rbowtie2 Rhisat2 rlang Rsamtools S4Vectors shiny shinyFiles shinyjs ShortRead tidyr]; };
CiteFuse = derive2 { name="CiteFuse"; version="1.16.0"; sha256="1vxynidr7p0khq54d08vzzh2ijaxx1ghm7pxnpg7zppfxvlmsh35"; 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="3.8.0"; sha256="1z8sfj7jpzdfwd56xn8748aw1cs99fm3ai6clkx7dmn2zhm1l04d"; depends=[BiocParallel dplyr genefilter generics ggplot2 ggpubr ggupset MultiAssayExperiment ranger reshape2 rlang S4Vectors survival tidyr]; };
ClassifyR = derive2 { name="ClassifyR"; version="3.8.2"; sha256="1p78lxcannrfif2029pksc1minzf4jp0p4r79b7rz06p3nq54wav"; depends=[BiocParallel dplyr genefilter generics ggplot2 ggpubr ggupset MultiAssayExperiment ranger reshape2 rlang S4Vectors survival tidyr]; };
Clomial = derive2 { name="Clomial"; version="1.40.0"; sha256="17n0s9ppjfcvzb6fyyny61r1hdh4vyf6nf1yjd01vnw8wzyy01f6"; depends=[matrixStats permute]; };
CluMSID = derive2 { name="CluMSID"; version="1.20.0"; sha256="02y79fhzx2hzwj8sjafywm7zqqar48b1m156ld60jjvskrv8ywqf"; depends=[ape Biobase dbscan GGally ggplot2 gplots MSnbase mzR network plotly RColorBrewer S4Vectors sna]; };
ClustAll = derive2 { name="ClustAll"; version="1.0.0"; sha256="13qg0r6lqvzyggkf8gjyxh8d871f483fcrhgbhr4xwpfpwssv8k8"; depends=[bigstatsr circlize cluster clValid ComplexHeatmap doSNOW dplyr FactoMineR flock foreach fpc ggplot2 mice modeest networkD3 pbapply RColorBrewer]; };
@ -249,7 +250,7 @@ in with self; {
CytoPipeline = derive2 { name="CytoPipeline"; version="1.4.0"; sha256="1c8w2v8990z8kp7wxc69ildhj0v5g3zx05dzyhb16nrlnb7bfcc4"; depends=[BiocFileCache BiocParallel diagram flowAI flowCore ggcyto ggplot2 jsonlite PeacoQC rlang scales withr]; };
CytoPipelineGUI = derive2 { name="CytoPipelineGUI"; version="1.2.0"; sha256="1xr7c8gcccxz8zl74amh35r2va3g58c2lwvl1j9py5g8ipmwprzj"; depends=[CytoPipeline flowCore ggplot2 plotly shiny]; };
DAMEfinder = derive2 { name="DAMEfinder"; version="1.16.0"; sha256="1ffqa7a3a0f3m58j6al2hd7aa8bamv4z170y4yn1vr1f8jrb7kq5"; depends=[BiocGenerics Biostrings bumphunter cowplot GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 IRanges limma plyr readr reshape2 Rsamtools S4Vectors stringr SummarizedExperiment VariantAnnotation]; };
DAPAR = derive2 { name="DAPAR"; version="1.36.1"; sha256="0cm129sarvbp7bk166msy79zicn52csfz22f7qaybx1azbm51qpq"; depends=[Biobase DAPARdata foreach highcharter MSnbase]; };
DAPAR = derive2 { name="DAPAR"; version="1.36.2"; sha256="1800c6g39gg9q43v1s5r13qm4aj53x18qzbbyz75fpwrril967gr"; depends=[Biobase DAPARdata foreach highcharter MSnbase]; };
DART = derive2 { name="DART"; version="1.52.0"; sha256="1zqzcssiibb9cl1iv6rzfmwlcms2llina41j5lkx0i9s8xmrqi06"; depends=[igraph]; };
DCATS = derive2 { name="DCATS"; version="1.2.0"; sha256="1hf275h40d5ggya58malxbrmzqi5gi04w847gc567qzpzs1bqfp2"; depends=[aod e1071 matrixStats MCMCpack robustbase]; };
DECIPHER = derive2 { name="DECIPHER"; version="3.0.0"; sha256="1bgzl3sy4l5xfgxrkw8z1dvygkn2dgcl2fl9ah13ggs8hc9h9nlm"; depends=[Biostrings DBI IRanges S4Vectors XVector]; };
@ -274,7 +275,7 @@ in with self; {
DMCHMM = derive2 { name="DMCHMM"; version="1.26.0"; sha256="0rv1v08nf7vbxci28j68sjxq77lj0swis26ryxp156alr397jfby"; depends=[BiocParallel calibrate fdrtool GenomicRanges IRanges multcomp rtracklayer S4Vectors SummarizedExperiment]; };
DMRScan = derive2 { name="DMRScan"; version="1.26.0"; sha256="0j68kxzmn3kskqy88j1dqznigiw1rb3b14hwnvcmyckmyhiysx73"; depends=[GenomeInfoDb GenomicRanges IRanges MASS Matrix mvtnorm RcppRoll]; };
DMRcaller = derive2 { name="DMRcaller"; version="1.36.0"; sha256="0r9xm77y6xs4mginwfshnpvn2l8phpag35a8mcasj63aqs05js2h"; depends=[betareg GenomicRanges IRanges Rcpp RcppRoll S4Vectors]; };
DMRcate = derive2 { name="DMRcate"; version="3.0.0"; sha256="1s83p6chchsx68qsfzqclpl3wq6fqy2r3namr8l3rrxp9b49342i"; depends=[AnnotationHub biomaRt bsseq edgeR ExperimentHub GenomeInfoDb GenomicRanges Gviz IRanges limma minfi missMethyl plyr S4Vectors SummarizedExperiment]; };
DMRcate = derive2 { name="DMRcate"; version="3.0.1"; sha256="091bj5dkcqci032x01cnzryjjy5cw6l4cci9mlll0bm2g4l4k7p5"; depends=[AnnotationHub biomaRt bsseq edgeR ExperimentHub GenomeInfoDb GenomicRanges Gviz IRanges limma minfi missMethyl plyr S4Vectors SummarizedExperiment]; };
DNABarcodeCompatibility = derive2 { name="DNABarcodeCompatibility"; version="1.20.0"; sha256="0iiy81svi1nnghaimnc5hs1prrk1z5kgv1bd5naysb8fpagd0jgl"; depends=[DNABarcodes dplyr numbers purrr stringr tidyr]; };
DNABarcodes = derive2 { name="DNABarcodes"; version="1.34.0"; sha256="0vxxg6fkgck640p9plk4vx3d05794s3xgxksv819d2wicvyby4hk"; depends=[BH Matrix Rcpp]; };
DNAcopy = derive2 { name="DNAcopy"; version="1.78.0"; sha256="1q4s6rb6iv9cmfkjymgdyb4h3z0x0kzzd2bvfdjrzzzza6vhjpxl"; depends=[]; };
@ -285,6 +286,7 @@ in with self; {
DSS = derive2 { name="DSS"; version="2.52.0"; sha256="1y9xg6ic3a03xswyfvyxdhnd7ngkljc96bm5fry4ni6kpa77bkv8"; depends=[Biobase BiocParallel bsseq]; };
DTA = derive2 { name="DTA"; version="2.50.0"; sha256="0njm0v10s31sx7v35kdv44815yy6k9h814s9zn98ld5qcrzn2q77"; depends=[LSD scatterplot3d]; };
DaMiRseq = derive2 { name="DaMiRseq"; version="2.16.0"; sha256="029idkjbha250f8wgwy6sjnjvlxqs0lkwal066693mc2h40rql11"; depends=[arm caret corrplot DESeq2 e1071 EDASeq edgeR FactoMineR FSelector ggplot2 Hmisc ineq kknn limma lubridate MASS pheatmap pls plsVarSel plyr randomForest RColorBrewer reshape2 RSNNS SummarizedExperiment sva]; };
Damsel = derive2 { name="Damsel"; version="1.0.0"; sha256="0n60wkrwk1npg1361x5plam6rabmqzlxdcij1qf5q351wfkqlp8y"; depends=[AnnotationDbi Biostrings dplyr edgeR GenomeInfoDb GenomicFeatures GenomicRanges ggbio ggplot2 goseq magrittr patchwork plyranges reshape2 rlang Rsamtools Rsubread stringr tidyr]; };
DeMAND = derive2 { name="DeMAND"; version="1.34.0"; sha256="0pdqgb4fsqzwhan1hwb4hi326yh5xhxwqkdqlffzhgfkp4lwi1cb"; depends=[KernSmooth]; };
DeMixT = derive2 { name="DeMixT"; version="1.20.0"; sha256="1hnaaidmflyh768pc1ivlq8rfjh5vrwycc0r6k1cyiinm53vknns"; depends=[base64enc dendextend DSS ggplot2 KernSmooth knitr matrixcalc matrixStats psych Rcpp rmarkdown SummarizedExperiment sva truncdist]; };
DeProViR = derive2 { name="DeProViR"; version="1.0.0"; sha256="0m1nhzq5kl6jyi3d8fzb77iplzc4p85v7lj5q7i7125kjv6bycsm"; depends=[BiocFileCache caret data_table dplyr fmsb ggplot2 keras pROC PRROC readr]; };
@ -363,7 +365,7 @@ in with self; {
GA4GHshiny = derive2 { name="GA4GHshiny"; version="1.26.0"; sha256="1vj0p1akcgzq2q43yir0g2klggjw8970chhzibw7yb5qxr2fz9ai"; depends=[AnnotationDbi BiocGenerics dplyr DT GA4GHclient GenomeInfoDb GenomicFeatures openxlsx purrr S4Vectors shiny shinyjs shinythemes tidyr]; };
GARS = derive2 { name="GARS"; version="1.24.0"; sha256="1wi56b6h1fi1rr4hrpbby6iwgax36q01h6hr2nm4bgb7cx6l3bii"; depends=[cluster DaMiRseq ggplot2 MLSeq SummarizedExperiment]; };
GAprediction = derive2 { name="GAprediction"; version="1.30.0"; sha256="0p38ivjzp0nsyr85a323xgjwb2amsmvr10ajq9m51z9acl4jzakx"; depends=[glmnet Matrix]; };
GBScleanR = derive2 { name="GBScleanR"; version="1.8.0"; sha256="0qmnlvra9fx9xja1al1iqz8rdh4w7q1w2h0z8wslladadv614ihv"; depends=[expm gdsfmt ggplot2 Rcpp RcppParallel SeqArray tidyr]; };
GBScleanR = derive2 { name="GBScleanR"; version="1.8.18"; sha256="1il1h9njfvhi4kxn30bhc31nkmr91b9imfafq68ccz947ckzhkpm"; depends=[expm gdsfmt ggplot2 Rcpp RcppParallel SeqArray tidyr]; };
GDCRNATools = derive2 { name="GDCRNATools"; version="1.24.0"; sha256="1grhgzl08f2infvvpd5084mvplvgqb0qa7d6afrfv6n5wigwnvbv"; 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="1.24.0"; sha256="0s78y646vr1m2lcsg91yy5xzc328hfbx0lnzyfg9pavp0d12yzip"; depends=[BiocGenerics DelayedArray gdsfmt S4Vectors SeqArray SNPRelate]; };
GEM = derive2 { name="GEM"; version="1.30.0"; sha256="1idp44h5szwwradv6i4bkgy055gaa04d5sxrv0r683h717pqagh5"; depends=[ggplot2]; };
@ -400,7 +402,7 @@ in with self; {
GSEAmining = derive2 { name="GSEAmining"; version="1.14.0"; sha256="1qzvmji5qn25q3lgb06k0dsxcn65krsrsrh6n06azz8ybkja9sj6"; depends=[dendextend dplyr ggplot2 ggwordcloud gridExtra rlang stringr tibble tidytext]; };
GSRI = derive2 { name="GSRI"; version="2.52.0"; sha256="0b8r1cih0zn8aj9nbpmqwiiqfhk9a2f0bxcqyx77g5jlg9b504kq"; depends=[Biobase fdrtool genefilter GSEABase les]; };
GSReg = derive2 { name="GSReg"; version="1.38.0"; sha256="1wfapjggz0qnaq9cg30d51c0zm5z6bhhf764qwgcbs9ngyjfwbvx"; depends=[AnnotationDbi GenomicFeatures Homo_sapiens org_Hs_eg_db]; };
GSVA = derive2 { name="GSVA"; version="1.52.2"; sha256="0b1lsmjf8azq9cg8pka1g94yxwib2dpbf29p9iq8csdid0c43ja7"; depends=[Biobase BiocParallel BiocSingular DelayedArray DelayedMatrixStats GSEABase HDF5Array IRanges Matrix S4Vectors SingleCellExperiment sparseMatrixStats SpatialExperiment SummarizedExperiment]; };
GSVA = derive2 { name="GSVA"; version="1.52.3"; sha256="08nxg3q350n5gf975r6b0zq4cr7lchv2i811crc4xbb7q39kw8k4"; depends=[Biobase BiocParallel BiocSingular DelayedArray DelayedMatrixStats GSEABase HDF5Array IRanges Matrix S4Vectors SingleCellExperiment sparseMatrixStats SpatialExperiment SummarizedExperiment]; };
GSgalgoR = derive2 { name="GSgalgoR"; version="1.14.0"; sha256="0mr0gdn5zkikjn5i5clq73vgmbnirl2abp84bjyzm5pf5dknjpmh"; depends=[cluster doParallel foreach matchingR nsga2R proxy survival]; };
GUIDEseq = derive2 { name="GUIDEseq"; version="1.34.0"; sha256="1xn44w1z1izzf2qr4xsmrvc468swjp6zmf4wxc33jbk5r9lv0n0x"; depends=[BiocGenerics Biostrings BSgenome ChIPpeakAnno CRISPRseek data_table dplyr GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 hash IRanges limma matrixStats multtest openxlsx patchwork purrr pwalign rio rlang Rsamtools S4Vectors stringr tidyr]; };
GWAS_BAYES = derive2 { name="GWAS.BAYES"; version="1.14.0"; sha256="05fp1wrddk9a961cx2ps0cad9rzagsyrfyfck6h1v3xb5gmz03ik"; depends=[caret GA limma MASS Matrix memoise]; };
@ -432,8 +434,8 @@ in with self; {
GenomicInteractionNodes = derive2 { name="GenomicInteractionNodes"; version="1.8.0"; sha256="1xkrmpsgqqsd470f4dgnbs5zb62qfrbpmzw97jsarri57pmqxy7a"; depends=[AnnotationDbi GenomeInfoDb GenomicFeatures GenomicRanges GO_db graph IRanges RBGL S4Vectors]; };
GenomicInteractions = derive2 { name="GenomicInteractions"; version="1.38.0"; sha256="16aaaa4nr1y5ng1hzw87q950clid28iqf4gkypcpihg3cz69axxg"; depends=[Biobase BiocGenerics data_table dplyr GenomeInfoDb GenomicRanges ggplot2 gridExtra Gviz igraph InteractionSet IRanges Rsamtools rtracklayer S4Vectors stringr]; };
GenomicOZone = derive2 { name="GenomicOZone"; version="1.18.0"; sha256="0i130gwf2ifgm635dhshfmnj97jqlz5nkwb98jbgz4ciq7mpdwv8"; depends=[biomaRt Ckmeans_1d_dp GenomeInfoDb GenomicRanges ggbio ggplot2 gridExtra IRanges lsr plyr Rdpack S4Vectors]; };
GenomicPlot = derive2 { name="GenomicPlot"; version="1.2.1"; sha256="0gx8kasidp0j5hcdc9yya1g4v5av21s9rb57wymxsqwv11rp5c5c"; depends=[BiocGenerics circlize ComplexHeatmap cowplot dplyr edgeR genomation GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 ggplotify ggpubr ggsci ggsignif IRanges plyranges RCAS Rsamtools rtracklayer scales tidyr txdbmaker VennDiagram viridis]; };
GenomicRanges = derive2 { name="GenomicRanges"; version="1.56.0"; sha256="18z890h4mwgizwqpz0hglgd0gmvv269cccb6i4rl3x93b519i0wx"; depends=[BiocGenerics GenomeInfoDb IRanges S4Vectors XVector]; };
GenomicPlot = derive2 { name="GenomicPlot"; version="1.2.2"; sha256="0s5slbkr6cpy5asl8v1fr914zgqg1q6gcwwf9nb0r8qh469c54pd"; depends=[BiocGenerics circlize ComplexHeatmap cowplot dplyr edgeR genomation GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 ggplotify ggpubr ggsci ggsignif IRanges plyranges RCAS Rsamtools rtracklayer scales tidyr txdbmaker VennDiagram viridis]; };
GenomicRanges = derive2 { name="GenomicRanges"; version="1.56.1"; sha256="0g0ld9i58pdxw2pwxi9nzj82mkryag457pvh6cvbvhb28pfamkma"; depends=[BiocGenerics GenomeInfoDb IRanges S4Vectors XVector]; };
GenomicScores = derive2 { name="GenomicScores"; version="2.16.0"; sha256="11sabicr2jm1cc9rdjr6vjqhf0gd9d7k04qlfhcdssvh02f957ia"; depends=[AnnotationHub Biobase BiocFileCache BiocGenerics BiocManager Biostrings DelayedArray GenomeInfoDb GenomicRanges HDF5Array httr IRanges rhdf5 S4Vectors XML]; };
GenomicSuperSignature = derive2 { name="GenomicSuperSignature"; version="1.12.0"; sha256="0prplxp7l7hx6697a18kk2s5iyrdgpqwfh79n9lnala2h2q3vhs0"; depends=[Biobase BiocFileCache ComplexHeatmap dplyr flextable ggplot2 ggpubr irlba plotly S4Vectors SummarizedExperiment]; };
GenomicTuples = derive2 { name="GenomicTuples"; version="1.38.0"; sha256="04inysn0aa2fmbnb01zk300x8qgz8bk4rhw68ka6ni7cbrn88ysa"; depends=[BiocGenerics data_table GenomeInfoDb GenomicRanges IRanges Rcpp S4Vectors]; };
@ -577,7 +579,7 @@ in with self; {
MGnifyR = derive2 { name="MGnifyR"; version="1.0.0"; sha256="0siqjril79bcbs90v7ng1j2rzrs4nl5y4wv1ih2cgp464n8agh6a"; depends=[ape BiocGenerics dplyr httr mia MultiAssayExperiment plyr reshape2 S4Vectors SummarizedExperiment tidyjson TreeSummarizedExperiment urltools]; };
MICSQTL = derive2 { name="MICSQTL"; version="1.2.2"; sha256="141dgc7k28ig9yw6km7ahjp0zyshg4kp3f6bs0ixnv6566dlb4c9"; depends=[BiocParallel dirmult ggplot2 ggpubr ggridges glue magrittr nnls purrr S4Vectors SummarizedExperiment TCA TOAST]; };
MIRA = derive2 { name="MIRA"; version="1.26.0"; sha256="05s4wm7cnjyb1sg6zawp5rxj23ym5kkh95cj79k6cx6l0fb946c0"; depends=[Biobase BiocGenerics bsseq data_table GenomicRanges ggplot2 IRanges S4Vectors]; };
MIRit = derive2 { name="MIRit"; version="1.0.0"; sha256="1c6zz24l2l362lkyha9ls7a990dpvpxskyzxz755zkf0q4cpdyn4"; depends=[AnnotationDbi BiocFileCache BiocParallel DESeq2 edgeR fgsea geneset ggplot2 ggpubr graph graphite httr limma MultiAssayExperiment Rcpp readxl Rgraphviz rlang]; };
MIRit = derive2 { name="MIRit"; version="1.0.0"; sha256="1c6zz24l2l362lkyha9ls7a990dpvpxskyzxz755zkf0q4cpdyn4"; depends=[AnnotationDbi BiocFileCache BiocParallel DESeq2 edgeR fgsea genekitr geneset ggplot2 ggpubr graph graphite httr limma MultiAssayExperiment Rcpp readxl Rgraphviz rlang]; };
MLInterfaces = derive2 { name="MLInterfaces"; version="1.84.0"; sha256="1m8clkb5rznzv2fwrl59csq8v0ibqwdm4fphq10b8pmyvj880qpn"; depends=[annotate Biobase BiocGenerics cluster fpc gbm gdata genefilter ggvis hwriter magrittr MASS mlbench pls RColorBrewer Rcpp rpart sfsmisc shiny SummarizedExperiment threejs]; };
MLP = derive2 { name="MLP"; version="1.52.0"; sha256="0ij15mcpahgykaalaj954qhk21gd967sngn2ad4wh4h6p99n6902"; depends=[AnnotationDbi gplots]; };
MLSeq = derive2 { name="MLSeq"; version="2.22.0"; sha256="0vm4giqqp2iq1w40nkn4bjc81ppdhqhbxq6w6ps3i2rdzwcq49ir"; depends=[Biobase caret DESeq2 edgeR foreach ggplot2 limma pamr plyr sSeq SummarizedExperiment testthat VennDiagram xtable]; };
@ -602,7 +604,7 @@ in with self; {
MSstatsPTM = derive2 { name="MSstatsPTM"; version="2.6.0"; sha256="0ivcxd2awrswih6n7is7zkcfrqiihk998g081krcp25i832xfqvh"; depends=[Biostrings checkmate data_table dplyr ggplot2 ggrepel gridExtra MSstats MSstatsConvert MSstatsTMT Rcpp stringi stringr]; };
MSstatsQC = derive2 { name="MSstatsQC"; version="2.22.0"; sha256="0pp813mx6kwmxyyi67qsak09k012nn05pv60ndx8x6dq9ph8aghn"; depends=[dplyr ggExtra ggplot2 MSnbase plotly qcmetrics]; };
MSstatsQCgui = derive2 { name="MSstatsQCgui"; version="1.24.0"; sha256="0kjidspplam63367yc09a17a3gq52rbmfrcnaxnxpiwkl7mphzz0"; depends=[dplyr ggExtra gridExtra MSstatsQC plotly shiny]; };
MSstatsShiny = derive2 { name="MSstatsShiny"; version="1.6.0"; sha256="0a1x5b97rvbk7j80y8lranh3fkhrlcbsk884fj3w49wh6cjs8pph"; depends=[data_table dplyr DT ggplot2 ggrepel gplots Hmisc htmltools marray mockery MSstats MSstatsConvert MSstatsPTM MSstatsTMT plotly readxl shiny shinyBS shinybusy shinyjs tidyr uuid]; };
MSstatsShiny = derive2 { name="MSstatsShiny"; version="1.6.2"; sha256="0h79yy5b9n2kfpbc3fhfajfmrqdzghj3ycaparn1v1dzjmi87z9y"; depends=[data_table dplyr DT ggplot2 ggrepel gplots Hmisc htmltools marray mockery MSstats MSstatsConvert MSstatsPTM MSstatsTMT plotly readxl shiny shinyBS shinybusy shinyjs tidyr uuid]; };
MSstatsTMT = derive2 { name="MSstatsTMT"; version="2.12.1"; sha256="03nnwh5qbr3wd942yj5xa2gd2bk28ncxq2dri3my5gwsrlfxfxpn"; depends=[checkmate data_table ggplot2 htmltools limma lme4 lmerTest MSstats MSstatsConvert plotly]; };
MVCClass = derive2 { name="MVCClass"; version="1.78.0"; sha256="1wi6acw51q48v149l72b2pp0iyjrwq1bbmr53y3m609xfadg4qim"; depends=[]; };
MWASTools = derive2 { name="MWASTools"; version="1.28.0"; sha256="1k72ycx0zlflcfpqapvh9m6mk3vc9wl0pbsi4jbcdigl6vx1zixv"; depends=[boot car ComplexHeatmap ggplot2 glm2 gridExtra igraph KEGGgraph KEGGREST ppcor qvalue RCurl SummarizedExperiment]; };
@ -644,7 +646,7 @@ in with self; {
MinimumDistance = derive2 { name="MinimumDistance"; version="1.48.0"; sha256="1pqf2q5hxjb1dwg981aldl0sw10f86yszp6z511vzx1y70ca6j3h"; depends=[Biobase BiocGenerics data_table DNAcopy ff foreach GenomeInfoDb GenomicRanges IRanges lattice MatrixGenerics matrixStats oligoClasses S4Vectors SummarizedExperiment VanillaICE]; };
ModCon = derive2 { name="ModCon"; version="1.12.0"; sha256="06v2ka7rhiqnjdgb7ky6ps2b90j29y1yqsvkk24a6nsd2q8gpkil"; depends=[data_table]; };
Modstrings = derive2 { name="Modstrings"; version="1.20.0"; sha256="0yc8gsgxlww2g9z1m6jl02aqmama10fkr2mvibvdi01s5pqwdbky"; depends=[BiocGenerics Biostrings crayon GenomicRanges IRanges S4Vectors stringi stringr XVector]; };
MoleculeExperiment = derive2 { name="MoleculeExperiment"; version="1.4.0"; sha256="0p3hbp375d53pbgbv87nzy0jaiml1ywl8sf4l0m38ksz4yg36vir"; depends=[BiocParallel cli data_table dplyr EBImage ggplot2 magrittr Matrix purrr rhdf5 rjson rlang S4Vectors SpatialExperiment terra]; };
MoleculeExperiment = derive2 { name="MoleculeExperiment"; version="1.4.1"; sha256="0w539058lm99z53lkjf9ljk1dr4fp150a9cwa9s9xrax90wpmy6j"; depends=[BiocParallel cli data_table dplyr EBImage ggplot2 magrittr Matrix purrr rhdf5 rjson rlang S4Vectors SpatialExperiment terra]; };
Moonlight2R = derive2 { name="Moonlight2R"; version="1.2.0"; sha256="0ff37hjp3llf875z4wym60vanda6gbysqmcp90dcbl33bx0fynja"; depends=[AnnotationHub Biobase BiocGenerics circlize clusterProfiler ComplexHeatmap doParallel DOSE dplyr easyPubMed EpiMix ExperimentHub foreach fuzzyjoin GenomicRanges GEOquery ggplot2 gplots HiveR magrittr org_Hs_eg_db parmigene purrr qpdf randomForest RColorBrewer readr RISmed rtracklayer seqminer stringr tibble tidyHeatmap tidyr]; };
MoonlightR = derive2 { name="MoonlightR"; version="1.30.0"; sha256="0jhc7y01qrz3cg2jnjqwgi5cgrh6616q9k3f3hldkq0x6z0z1vwn"; depends=[Biobase circlize clusterProfiler doParallel DOSE foreach GEOquery gplots HiveR limma parmigene randomForest RColorBrewer RISmed SummarizedExperiment TCGAbiolinks]; };
Motif2Site = derive2 { name="Motif2Site"; version="1.8.0"; sha256="03rjhrxi016q0k7dzbfwr192sgc6z5kjyqdd6qzdajkpgq6dpi2m"; depends=[BiocGenerics Biostrings BSgenome edgeR GenomeInfoDb GenomicAlignments GenomicRanges IRanges MASS mixtools S4Vectors]; };
@ -662,7 +664,7 @@ in with self; {
MsQuality = derive2 { name="MsQuality"; version="1.4.0"; sha256="1khpjzzrrd2b7ngwq43y3sgndmrr6l8f504lyakr46xr1vyzppsl"; depends=[BiocParallel ggplot2 htmlwidgets msdata MsExperiment plotly ProtGenerics rlang rmzqc shiny shinydashboard Spectra stringr tibble tidyr]; };
MuData = derive2 { name="MuData"; version="1.8.0"; sha256="0kjin6cfw9aipghd0imi2play19czplwcz2gi5akv6gk9wy98k8x"; depends=[DelayedArray Matrix MultiAssayExperiment rhdf5 S4Vectors SingleCellExperiment SummarizedExperiment]; };
Mulcom = derive2 { name="Mulcom"; version="1.54.0"; sha256="1sb6g08k1wlnjiiw9a7hm34izbnh8ar1mh6vxc0jzkwk6522nva2"; depends=[Biobase fields]; };
MultiAssayExperiment = derive2 { name="MultiAssayExperiment"; version="1.30.1"; sha256="07sfcc2cd68qmspcm4ypp3cg05d20fbpwiz5ik4lqsa0hw0j2dhw"; depends=[Biobase BiocBaseUtils BiocGenerics DelayedArray GenomicRanges IRanges S4Vectors SummarizedExperiment tidyr]; };
MultiAssayExperiment = derive2 { name="MultiAssayExperiment"; version="1.30.2"; sha256="1j74ql0lz2xf0jsf4cjfapdmxbf6hb22699d3dyj8gwd1s92myjz"; depends=[Biobase BiocBaseUtils BiocGenerics DelayedArray GenomicRanges IRanges S4Vectors SummarizedExperiment tidyr]; };
MultiBaC = derive2 { name="MultiBaC"; version="1.14.0"; sha256="0m08620sii9181y0vlcrw9nbcnp4vnjjxvp96iqlgg5fsb23wbl7"; depends=[ggplot2 Matrix MultiAssayExperiment pcaMethods plotrix ropls]; };
MultiDataSet = derive2 { name="MultiDataSet"; version="1.32.0"; sha256="1y1j5svi52cvixjsn13122kvd0z0c7zfki3p6rr8wjd5w7riiyqw"; depends=[Biobase BiocGenerics GenomicRanges ggplot2 ggrepel IRanges limma qqman S4Vectors SummarizedExperiment]; };
MultiMed = derive2 { name="MultiMed"; version="2.26.0"; sha256="03qcqzkh5jiy46613g29bs7dipgzzparwdcllw1lwssh4y8fvwc0"; depends=[]; };
@ -756,7 +758,7 @@ in with self; {
Pigengene = derive2 { name="Pigengene"; version="1.30.0"; sha256="08jgn7cx3gvxsih8jp9xh1irf7f0j0yfw4srbc6ynffc0197papc"; depends=[BiocStyle bnlearn C50 clusterProfiler DBI DOSE dplyr gdata ggplot2 GO_db graph impute MASS matrixStats openxlsx partykit pheatmap preprocessCore ReactomePA Rgraphviz WGCNA]; };
PoDCall = derive2 { name="PoDCall"; version="1.12.0"; sha256="121clnkr598p7iy91s0dp76ammz853p2cds0zy15pjj8n21rc7lv"; depends=[diptest DT ggplot2 gridExtra LaplacesDemon mclust purrr readr rlist shiny shinyjs]; };
PrInCE = derive2 { name="PrInCE"; version="1.20.0"; sha256="173vakwqjalh2spz1f7qq6ngw8hjkqpj4zf0rx6xsnycjn54jip0"; depends=[Biobase dplyr forecast Hmisc LiblineaR magrittr MSnbase naivebayes progress purrr ranger Rdpack robustbase speedglm tester tidyr]; };
Prostar = derive2 { name="Prostar"; version="1.36.1"; sha256="08pgvgl7781x9rvl3cg7pm4155y5yrk3j35667z9i3p0na8wmxvw"; depends=[Biobase colourpicker DAPAR DAPARdata data_table DT future ggplot2 gplots gtools highcharter htmlwidgets later markdown promises R_utils rclipboard RColorBrewer rhandsontable sass shiny shinyAce shinyBS shinycssloaders shinyjqui shinyjs shinythemes shinyTree shinyWidgets tibble vioplot webshot XML]; };
Prostar = derive2 { name="Prostar"; version="1.36.2"; sha256="140whr7klab1as5y8h9lbmlgn4f63kfdfhzjyxjp8pk3aq1xv53i"; depends=[Biobase colourpicker DAPAR DAPARdata data_table DT future ggplot2 gplots gtools highcharter htmlwidgets later markdown promises R_utils rclipboard RColorBrewer rhandsontable sass shiny shinyAce shinyBS shinycssloaders shinyjqui shinyjs shinythemes shinyTree shinyWidgets tibble vioplot webshot XML]; };
ProtGenerics = derive2 { name="ProtGenerics"; version="1.36.0"; sha256="0h0i4dgsgvyhma5pfvycv6wyxv27vp0b2i8b6l8hj55z8cvmvfln"; depends=[]; };
ProteoDisco = derive2 { name="ProteoDisco"; version="1.10.0"; sha256="10cdniinadihp4acdz22c0zjg3if3rqn9cy753f2x1nq539n3vql"; depends=[BiocGenerics BiocParallel Biostrings checkmate cleaver dplyr GenomeInfoDb GenomicFeatures GenomicRanges IRanges ParallelLogger plyr rlang S4Vectors tibble tidyr VariantAnnotation XVector]; };
ProteoMM = derive2 { name="ProteoMM"; version="1.22.0"; sha256="173nqg0nqdgy7z9qklxk88lxmhj7qf8jjcidpllf9hap9y1lk910"; depends=[biomaRt gdata ggplot2 ggrepel gtools matrixStats]; };
@ -911,6 +913,7 @@ in with self; {
SIMLR = derive2 { name="SIMLR"; version="1.30.0"; sha256="18mld0yvkmy1znsv3dkch6f8x9h9j20zm3qq84ggw0wsbgrrcm1z"; depends=[Matrix pracma Rcpp RcppAnnoy RSpectra]; };
SLqPCR = derive2 { name="SLqPCR"; version="1.70.0"; sha256="0xr0kjy2bn8cprj4p7c9bi7wsrvfx6bxymnvdz5c50s9hc35h2ky"; depends=[]; };
SMAD = derive2 { name="SMAD"; version="1.20.0"; sha256="0rj4f38nlr3a5fmf0dqhqi7iln78lkvghv4w8yr2kcavnsl4lzar"; depends=[dplyr magrittr Rcpp RcppAlgos tidyr]; };
SMITE = derive2 { name="SMITE"; version="1.32.0"; sha256="0dp4yas2gdwnvvbxdkid61j9c2a32cfcn3iw9nwijp6aqlv9rrv9"; depends=[AnnotationDbi Biobase BioNet geneLenDataBase GenomicRanges ggplot2 goseq Hmisc igraph IRanges KEGGREST org_Hs_eg_db plyr reactome_db S4Vectors scales]; };
SNAGEE = derive2 { name="SNAGEE"; version="1.44.0"; sha256="001afmi0hpjih8h8dl5w0llmccgd9g7lrz80fs7m2f3avz9hf2lc"; depends=[SNAGEEdata]; };
SNPRelate = derive2 { name="SNPRelate"; version="1.38.0"; sha256="0znk9vvnahkypmkrx82r1ryp41xr675b4ddpgx0nl3708xhncz5f"; depends=[gdsfmt]; };
SNPediaR = derive2 { name="SNPediaR"; version="1.30.0"; sha256="1p33fmjdpscc42wicx23xg1jbg2m18msf4rhg9pr52n6yzr42b8v"; depends=[jsonlite RCurl]; };
@ -925,8 +928,8 @@ in with self; {
SQLDataFrame = derive2 { name="SQLDataFrame"; version="1.18.0"; sha256="1fdf6dvrkg5cjnlh9466dnmqjfg7dq7dj06qjc61zyshlvslxlwh"; depends=[BiocGenerics DBI DelayedArray duckdb RSQLite S4Vectors]; };
SRAdb = derive2 { name="SRAdb"; version="1.66.0"; sha256="0qvqixmn8am90a4n5ydva630kkxr735y6kdcikp1q0k8pxxvbm0j"; depends=[GEOquery graph RCurl RSQLite]; };
STATegRa = derive2 { name="STATegRa"; version="1.40.0"; sha256="1m78hixyjavvryfcyd5g3f898r7hcn1cwdwbv3i2b9yj7z6r7knv"; depends=[affy Biobase calibrate edgeR foreach ggplot2 gplots gridExtra limma MASS]; };
STRINGdb = derive2 { name="STRINGdb"; version="2.16.0"; sha256="1bn21hqvcl1a4knj7iygwqx79s49ggjaw30fj6478h7khha6556b"; depends=[gplots hash httr igraph plotrix plyr png RColorBrewer sqldf]; };
STdeconvolve = derive2 { name="STdeconvolve"; version="1.8.0"; sha256="0pyyxmh4bnavsdw6riv72y5m8l53mfr0lpiy9mh0qn57rlmw5fr9"; depends=[BiocParallel clue ggplot2 liger Matrix mgcv reshape2 scatterpie slam topicmodels viridis]; };
STRINGdb = derive2 { name="STRINGdb"; version="2.16.4"; sha256="02fim09w9s38hvgp1g3fxqabd5r2fjysljlfrya2nr17drqkzqyx"; depends=[gplots hash httr igraph plotrix plyr png RColorBrewer sqldf]; };
STdeconvolve = derive2 { name="STdeconvolve"; version="1.8.0"; sha256="0pyyxmh4bnavsdw6riv72y5m8l53mfr0lpiy9mh0qn57rlmw5fr9"; depends=[BiocParallel clue ggplot2 Matrix mgcv reshape2 scatterpie slam topicmodels viridis]; };
SUITOR = derive2 { name="SUITOR"; version="1.6.0"; sha256="0wricb7fi87lrmasljhz0l7ya22yq3a2c6654k4v3x11z9zb2pl6"; depends=[BiocParallel ggplot2]; };
SVMDO = derive2 { name="SVMDO"; version="1.4.0"; sha256="11cn7kffgssbjk307vxjr6i2cs94fn6hhz09dbx5qgg89m4gsdgi"; depends=[AnnotationDbi BSDA caret caTools data_table DOSE dplyr e1071 golem klaR nortest org_Hs_eg_db shiny shinyFiles shinytitle sjmisc SummarizedExperiment survival]; };
SWATH2stats = derive2 { name="SWATH2stats"; version="1.34.0"; sha256="052nzh5rhq3sp6vyibbiz2li32lnd5c719kqkdhwjsc8y3pcir00"; depends=[biomaRt data_table ggplot2 reshape2]; };
@ -971,7 +974,7 @@ in with self; {
SpliceWiz = derive2 { name="SpliceWiz"; version="1.6.0"; sha256="11pad2gdra4bq6is34d7981f6vb4wzsmvihgf08514d1598qn1cc"; 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]; };
SplicingFactory = derive2 { name="SplicingFactory"; version="1.12.0"; sha256="1iwkkbxviain77a64x41hc97c9bl77ayjpbjpkvmhwjh4hfdl9b7"; depends=[SummarizedExperiment]; };
SplicingGraphs = derive2 { name="SplicingGraphs"; version="1.44.0"; sha256="1k4j23i7ffw1q18y48jhhj7g5k3vjihq619np2y7p7xc9wv0d45g"; depends=[BiocGenerics BiocParallel GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges graph igraph IRanges Rgraphviz Rsamtools S4Vectors]; };
SpotClean = derive2 { name="SpotClean"; version="1.6.0"; sha256="1mxw6gjjdg7a1g30gcwkr1k4zys0bwqlmh8wv4p6jfa2hcxa0cza"; depends=[dplyr ggplot2 Matrix RColorBrewer readbitmap rhdf5 rjson rlang S4Vectors Seurat SpatialExperiment SummarizedExperiment tibble viridis]; };
SpotClean = derive2 { name="SpotClean"; version="1.6.1"; sha256="1wq1igfyadmzszacnwx8rfhm82xslzqzjkvx6xigs1fng0c7yn61"; depends=[dplyr ggplot2 Matrix RColorBrewer readbitmap rhdf5 rjson rlang S4Vectors Seurat SpatialExperiment SummarizedExperiment tibble viridis]; };
SpotSweeper = derive2 { name="SpotSweeper"; version="1.0.0"; sha256="1jkc37ymip3r29fh041mfa2bq17qhxq7mp0i35zrjh2lzm83qxas"; depends=[BiocNeighbors escheR ggplot2 MASS SingleCellExperiment spatialEco SpatialExperiment SummarizedExperiment]; };
Statial = derive2 { name="Statial"; version="1.6.0"; sha256="0lzr0vc4zl5ryhs17l866w261ya9kxm7hx86g6xv16wr6fbw3mgv"; 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="1.50.0"; sha256="0biizsjg9ysr2d1kyh962znikvgwli0zf0jn8khbs4prakjxmjyn"; depends=[BiocGenerics graph RBGL]; };
@ -1016,7 +1019,7 @@ in with self; {
TVTB = derive2 { name="TVTB"; version="1.30.0"; sha256="0in5l9nq0br7c1n546wn29av5m25xxc82hvns5z8mshnnlk59pmn"; depends=[AnnotationFilter BiocGenerics BiocParallel Biostrings ensembldb ensemblVEP GenomeInfoDb GenomicRanges GGally ggplot2 Gviz IRanges limma reshape2 Rsamtools S4Vectors SummarizedExperiment VariantAnnotation]; };
TargetDecoy = derive2 { name="TargetDecoy"; version="1.10.0"; sha256="1gys5v5sb3ypip82q9gw21dg5whllqdhh8i9zy48qrg4mh2jby1s"; depends=[ggplot2 ggpubr miniUI mzID mzR shiny]; };
TargetScore = derive2 { name="TargetScore"; version="1.42.0"; sha256="124fy7q7y37jxasvnlk8sfkw307qs1wyafxvs3fmb3f3impffxsz"; depends=[Matrix pracma]; };
TargetSearch = derive2 { name="TargetSearch"; version="2.6.0"; sha256="0wb7wagjdz03a72x6lwl5a0hr7ps4zw3vf7bc5ipgvp46a4nbdrh"; depends=[assertthat ncdf4]; };
TargetSearch = derive2 { name="TargetSearch"; version="2.6.1"; sha256="1q6v6pfkpcm23a39vgp9ysbqa6wwkwv9dgnxd6m8gjlq3azgsnf6"; depends=[assertthat ncdf4]; };
TileDBArray = derive2 { name="TileDBArray"; version="1.14.0"; sha256="1hgwcxffg50nfjb3bpl00h7vhmfs1x15ly7sd0lpcnamk7f9c003"; depends=[DelayedArray Rcpp S4Vectors tiledb]; };
TissueEnrich = derive2 { name="TissueEnrich"; version="1.24.1"; sha256="02amlvaf5v30x2swxhi4na4c623v00gb3q1bvlcqias9gaaizzim"; depends=[dplyr ggplot2 GSEABase SummarizedExperiment tidyr]; };
TitanCNA = derive2 { name="TitanCNA"; version="1.42.0"; sha256="18ihvqn07g677r3facf43m69bnjx4i0s6w41h4mdn82hal0pfsx0"; depends=[BiocGenerics data_table dplyr foreach GenomeInfoDb GenomicRanges IRanges VariantAnnotation]; };
@ -1112,7 +1115,7 @@ in with self; {
anota2seq = derive2 { name="anota2seq"; version="1.26.0"; sha256="140k37wswl4w2136pz9y0z82sphzxmgzgk3cr400kkm39wjn7vxm"; depends=[DESeq2 edgeR limma multtest qvalue RColorBrewer SummarizedExperiment]; };
antiProfiles = derive2 { name="antiProfiles"; version="1.44.0"; sha256="0p2fhxzgn877mic2yv1sgcidgm74z8hxa3hdaawgvhhvi2j6v8wa"; depends=[locfit matrixStats]; };
apComplex = derive2 { name="apComplex"; version="2.70.0"; sha256="1fsqrds5r8bhdf7fbnw6rf3vqapl6xk1a5l6jjb98raxmjsrfyqs"; depends=[graph org_Sc_sgd_db RBGL Rgraphviz]; };
apeglm = derive2 { name="apeglm"; version="1.26.0"; sha256="0l84sf4ikx0q031wf0k26n9ikwmgs4nm7v7bky47q3ik29mh7wgs"; depends=[emdbook GenomicRanges Rcpp RcppEigen RcppNumerical SummarizedExperiment]; };
apeglm = derive2 { name="apeglm"; version="1.26.1"; sha256="039my876v0k2mr50w90w3phj4cq55awf5ks07kr2fnm7w211gxvs"; depends=[emdbook GenomicRanges Rcpp RcppEigen RcppNumerical SummarizedExperiment]; };
appreci8R = derive2 { name="appreci8R"; version="1.22.0"; sha256="1nwb7475lhclyd0jdwm0sp1wh2rgs2h16k4hin6z44axix5v7jhr"; depends=[Biostrings BSgenome BSgenome_Hsapiens_UCSC_hg19 COSMIC_67 DT GenomicFeatures GenomicRanges GenomicScores Homo_sapiens IRanges MafDb_1Kgenomes_phase3_hs37d5 MafDb_ExAC_r1_0_hs37d5 MafDb_gnomADex_r2_1_hs37d5 openxlsx PolyPhen_Hsapiens_dbSNP131 rentrez Rsamtools S4Vectors seqinr shiny shinyjs SIFT_Hsapiens_dbSNP137 SNPlocs_Hsapiens_dbSNP144_GRCh37 stringr SummarizedExperiment TxDb_Hsapiens_UCSC_hg19_knownGene VariantAnnotation XtraSNPlocs_Hsapiens_dbSNP144_GRCh37]; };
aroma_light = derive2 { name="aroma.light"; version="3.34.0"; sha256="1v24b43knsjpw44zkrzv8pvxjiw12rcz9wqp4ahd88dg23j7pvwz"; depends=[matrixStats R_methodsS3 R_oo R_utils]; };
arrayMvout = derive2 { name="arrayMvout"; version="1.62.0"; sha256="11v3s972nyahdswqdcab0fj9jb73vd5dnd5kfb09572y4z0hn5xw"; depends=[affy affyContam Biobase lumi mdqc parody]; };
@ -1122,7 +1125,7 @@ in with self; {
atSNP = derive2 { name="atSNP"; version="1.20.0"; sha256="08pcbys8iy8wzqzzvlnwc3qw7m7cswkqa3x2x2x8m4ni1s4isd6z"; depends=[BiocFileCache BiocParallel BSgenome data_table ggplot2 lifecycle motifStack rappdirs Rcpp testthat]; };
atena = derive2 { name="atena"; version="1.10.0"; sha256="1y2v8mi9awgfbcawpcir01qglxn0bdgj6v2dsdqp6if25cizl3sr"; depends=[AnnotationHub BiocGenerics BiocParallel cli GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges Matrix MatrixGenerics matrixStats Rsamtools S4Vectors sparseMatrixStats SQUAREM SummarizedExperiment]; };
attract = derive2 { name="attract"; version="1.56.0"; sha256="08l634sk6y06y2m78vsd0ld4w3h6qvx4hk6wkqflkl9jjyqpx8jy"; depends=[AnnotationDbi Biobase cluster GOstats KEGGREST limma org_Hs_eg_db reactome_db]; };
autonomics = derive2 { name="autonomics"; version="1.12.0"; sha256="0z2zzib4852ycnvrqiidyn6yq9wh06d7p5ssnhyydvwxp1gnwska"; depends=[abind BiocFileCache BiocGenerics bit64 codingMatrices colorspace data_table dplyr edgeR ggforce ggplot2 ggrepel gridExtra limma magrittr matrixStats MultiAssayExperiment R_utils RColorBrewer readxl rlang S4Vectors scales stringi SummarizedExperiment tidyr tidyselect vsn]; };
autonomics = derive2 { name="autonomics"; version="1.12.1"; sha256="1fzzj0v6v4jvr3wh5bnjr6h2ny8zfm9pdlbhq5syaa2plvsbblpy"; depends=[abind BiocFileCache BiocGenerics bit64 codingMatrices colorspace data_table dplyr edgeR ggforce ggplot2 ggrepel gridExtra limma magrittr matrixStats MultiAssayExperiment R_utils RColorBrewer readxl rlang S4Vectors scales stringi SummarizedExperiment tidyr tidyselect vsn]; };
awst = derive2 { name="awst"; version="1.12.0"; sha256="1iaakdjxrz4szl4lnjcszy47q5dsh2d7i3wrr3wwdhw6wjcd62hj"; depends=[SummarizedExperiment]; };
bacon = derive2 { name="bacon"; version="1.32.0"; sha256="09lvjb0fa70kcl7mkp4agxv6jcm2ncmnrffav6zmz038imhmvdgm"; depends=[BiocParallel ellipse ggplot2]; };
ballgown = derive2 { name="ballgown"; version="2.36.0"; sha256="0x3avbqf0ipmb70szf2chhbdg14ba2hwhyyz0wd66c1qwfk6aj9v"; depends=[Biobase GenomeInfoDb GenomicRanges IRanges limma RColorBrewer rtracklayer S4Vectors sva]; };
@ -1193,7 +1196,7 @@ in with self; {
cardelino = derive2 { name="cardelino"; version="1.6.0"; sha256="16mczwh41gf7ikbzxvggai7a8d64fn2k7q9w1yxf0sn6cwg3l0di"; depends=[combinat GenomeInfoDb GenomicRanges ggplot2 ggtree Matrix matrixStats pheatmap S4Vectors snpStats VariantAnnotation vcfR]; };
casper = derive2 { name="casper"; version="2.38.0"; sha256="0bwjnncm93j99m38mv99i1pw42cjmib4sqzw5nhb6p9mj39mm3zb"; depends=[Biobase BiocGenerics coda EBarrays gaga GenomeInfoDb GenomicFeatures GenomicRanges gtools IRanges limma mgcv Rsamtools rtracklayer S4Vectors sqldf survival VGAM]; };
categoryCompare = derive2 { name="categoryCompare"; version="1.48.0"; sha256="0mfmv3wna7dddf4i3ckh2iin8vq05g4fjb1n2pvw0s9lz3da3rjf"; depends=[annotate AnnotationDbi Biobase BiocGenerics Category colorspace GOstats graph GSEABase hwriter RCy3]; };
cbaf = derive2 { name="cbaf"; version="1.26.1"; sha256="0mw6pwsasvq5x8g4kqkm3qrwfz2iymsfbbj0m0jsrqgplqmb714l"; depends=[BiocFileCache cBioPortalData genefilter gplots openxlsx RColorBrewer]; };
cbaf = derive2 { name="cbaf"; version="1.26.3"; sha256="1lpz3n288v32nbb0g4jb1mxmx79amm29m40w3sfkgllnjjdwsyd3"; depends=[BiocFileCache cBioPortalData genefilter gplots openxlsx RColorBrewer]; };
cbpManager = derive2 { name="cbpManager"; version="1.12.0"; sha256="1idlxmnbyvc1nzshnvf3p4y9xdjb2kdcm05kpf3ihh993igddk14"; depends=[basilisk dplyr DT htmltools jsonlite magrittr markdown plyr rapportools reticulate rintrojs rlang shiny shinyBS shinycssloaders shinydashboard vroom]; };
ccImpute = derive2 { name="ccImpute"; version="1.6.0"; sha256="0pjdlh77wpv54m2kc26kyzmpqikgz666dkw5h6af7q7lmgp0xc19"; depends=[BiocParallel matrixStats Rcpp RcppEigen SIMLR]; };
ccfindR = derive2 { name="ccfindR"; version="1.24.0"; sha256="1n9dncj7d3ijk6h6fkgmh3a0c6xrfll2fifkl2bz26ndq9i4m1q9"; depends=[ape gtools irlba Matrix RColorBrewer Rcpp RcppEigen Rdpack Rmpi Rtsne S4Vectors SingleCellExperiment SummarizedExperiment]; };
@ -1318,7 +1321,7 @@ in with self; {
decontX = derive2 { name="decontX"; version="1.2.0"; sha256="0bxpzc9fib47c5prnshzykfd5a3mcik9n1ayd7jxygxy36icgqcj"; depends=[BH celda dbscan DelayedArray ggplot2 Matrix MCMCprecision patchwork plyr Rcpp RcppEigen RcppParallel reshape2 rstan rstantools S4Vectors scater Seurat SingleCellExperiment StanHeaders SummarizedExperiment withr]; };
decontam = derive2 { name="decontam"; version="1.24.0"; sha256="1xjd9jzxlj6gfd6fnygzm21q1wy5x5pl031sq1q0svq3jlnzvgb7"; depends=[ggplot2 reshape2]; };
deconvR = derive2 { name="deconvR"; version="1.10.0"; sha256="181dxjj8bzy1b9xq9hd3m3ak1698w7j0sf8h9g0bhf3blzlj4pmi"; depends=[assertthat BiocGenerics data_table dplyr e1071 foreach GenomicRanges IRanges magrittr MASS matrixStats methylKit minfi nnls quadprog rsq S4Vectors tidyr]; };
decoupleR = derive2 { name="decoupleR"; version="2.9.7"; sha256="0zi6shh1dn8kli66dyywwgy1s809yms0jrl6lkwvzn88rms7yaqb"; depends=[BiocParallel broom dplyr magrittr Matrix parallelly purrr rlang stringr tibble tidyr tidyselect withr]; };
decoupleR = derive2 { name="decoupleR"; version="2.10.0"; sha256="060ww5hlzk0dvh7a52i1nrz1s2xq5mmlw70rxpcs6d4j08k1cmic"; depends=[BiocParallel broom dplyr magrittr Matrix parallelly purrr rlang stringr tibble tidyr tidyselect withr]; };
deepSNV = derive2 { name="deepSNV"; version="1.50.0"; sha256="1rcq2bg4z6z7czqi662w5gsdc1vd4p8vb353hqayhciv31dz51fr"; depends=[Biostrings GenomicRanges IRanges Rhtslib SummarizedExperiment VariantAnnotation VGAM]; };
deltaCaptureC = derive2 { name="deltaCaptureC"; version="1.18.0"; sha256="019c6rlsl4glc4vkbz3kfcn9d9rh3vnfw0xbcsi33hk51z89qc78"; depends=[DESeq2 GenomicRanges ggplot2 IRanges SummarizedExperiment tictoc]; };
deltaGseg = derive2 { name="deltaGseg"; version="1.44.0"; sha256="0jdlcsajpksr58nj551r6biwir20k67ysa42bcingcrgii740yyk"; depends=[changepoint fBasics ggplot2 pvclust reshape scales tseries wavethresh]; };
@ -1348,7 +1351,7 @@ in with self; {
doseR = derive2 { name="doseR"; version="1.20.0"; sha256="09zr2r1vk1azrjwgx2bklv5sdypl3dba0szvh21nw1ndqyk9lwic"; depends=[digest edgeR lme4 matrixStats mclust RUnit S4Vectors SummarizedExperiment]; };
doubletrouble = derive2 { name="doubletrouble"; version="1.4.0"; sha256="0xfrpz3ilxapcclxgf7drkwcrhvn2d70fx6q139faslp1zs19bv0"; depends=[AnnotationDbi BiocParallel Biostrings GenomicFeatures GenomicRanges ggplot2 mclust MSA2dist rlang syntenet]; };
drawProteins = derive2 { name="drawProteins"; version="1.24.0"; sha256="1ap2lclwpr532pzapz61pd6lclq3d3idvq4462x19jaivnhf6mr5"; depends=[dplyr ggplot2 httr readr tidyr]; };
dreamlet = derive2 { name="dreamlet"; version="1.2.0"; sha256="096kjih2b1076sdv3nvha975lmbkibgbyp3xrnfxswjfjsh68rqr"; depends=[ashr beachmat BiocGenerics BiocParallel broom data_table DelayedArray DelayedMatrixStats dplyr edgeR ggbeeswarm ggplot2 ggrepel GSEABase gtools IRanges irlba limma lme4 mashr MASS Matrix MatrixGenerics metafor purrr Rcpp Rdpack remaCor reshape2 rlang S4Vectors scattermore SingleCellExperiment sparseMatrixStats SummarizedExperiment tidyr variancePartition zenith]; };
dreamlet = derive2 { name="dreamlet"; version="1.2.1"; sha256="06mpmwjxp7zs9fsggf2b3qc5vgmx6l5s7prl6l7b753zfq5gvjbg"; depends=[ashr beachmat BiocGenerics BiocParallel broom data_table DelayedArray DelayedMatrixStats dplyr edgeR ggbeeswarm ggplot2 ggrepel GSEABase gtools IRanges irlba limma lme4 mashr MASS Matrix MatrixGenerics metafor purrr Rcpp Rdpack remaCor reshape2 rlang S4Vectors scattermore SingleCellExperiment sparseMatrixStats SummarizedExperiment tidyr variancePartition zenith]; };
drugTargetInteractions = derive2 { name="drugTargetInteractions"; version="1.12.0"; sha256="079qy3mmv9skiybzh9ls3082wqb3r9x6fn50rgcwziapixlx2rh4"; depends=[AnnotationFilter BiocFileCache biomaRt dplyr ensembldb rappdirs RSQLite S4Vectors UniProt_ws]; };
dupRadar = derive2 { name="dupRadar"; version="1.34.0"; sha256="0wd03v3qqmprv1n8018w0qqaw0majhx2i33qam7vf4rm2ng1gcxj"; depends=[KernSmooth Rsubread]; };
dyebias = derive2 { name="dyebias"; version="1.64.0"; sha256="1k676kx37f6gdlrld2z7pygdf2cgin0d2cqgas83xizcq07ngnld"; depends=[Biobase marray]; };
@ -1373,7 +1376,7 @@ in with self; {
epigenomix = derive2 { name="epigenomix"; version="1.44.0"; sha256="1c1lwz5lbq69anpk1q7dhlfrvb66g8vrfyw7130x1c6y5yryk23k"; depends=[beadarray Biobase BiocGenerics GenomeInfoDb GenomicRanges IRanges MCMCpack Rsamtools S4Vectors SummarizedExperiment]; };
epigraHMM = derive2 { name="epigraHMM"; version="1.12.0"; sha256="1zkb81jd2gsj92yzlxhshaw4csap9b06gyy5gl1qi3k3qkx69dq9"; 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="1.8.0"; sha256="15lrkz7fqmjg5d2l77xbiqwdd3f2jnbw9nc6l4k6wglw3za3prr1"; 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]; };
epiregulon = derive2 { name="epiregulon"; version="1.0.0"; sha256="0gcg3ci4dn9jiz6avjgd3ss5lgpmqyll60lw62vzapgq5w1ap322"; depends=[AnnotationHub AUCell beachmat BiocParallel bluster BSgenome_Hsapiens_UCSC_hg19 BSgenome_Hsapiens_UCSC_hg38 BSgenome_Mmusculus_UCSC_mm10 checkmate entropy ExperimentHub GenomeInfoDb GenomicRanges IRanges lifecycle Matrix motifmatchr Rcpp S4Vectors scMultiome scran scuttle SingleCellExperiment SummarizedExperiment]; };
epiregulon = derive2 { name="epiregulon"; version="1.0.1"; sha256="0zhnra2kl1r2kh9g21fx3nqyb5sksnf7j81dzhjnwjvmlr52xp8w"; depends=[AnnotationHub AUCell beachmat BiocParallel bluster BSgenome_Hsapiens_UCSC_hg19 BSgenome_Hsapiens_UCSC_hg38 BSgenome_Mmusculus_UCSC_mm10 checkmate entropy ExperimentHub GenomeInfoDb GenomicRanges IRanges lifecycle Matrix motifmatchr Rcpp S4Vectors scMultiome scran scuttle SingleCellExperiment SummarizedExperiment]; };
epiregulon_extra = derive2 { name="epiregulon.extra"; version="1.0.0"; sha256="04d85zp0yadbxrjk88arnf64hfnw67yqn60y03a0wvrw6hcv1zdz"; depends=[checkmate circlize clusterProfiler ComplexHeatmap ggplot2 ggraph igraph lifecycle Matrix patchwork reshape2 scales scater scran SingleCellExperiment SummarizedExperiment]; };
epistack = derive2 { name="epistack"; version="1.10.0"; sha256="1kfviv9k43n6hy66x5r5hc2f7vb3y3v81qk1m9549nqvdii7ph5q"; depends=[BiocGenerics GenomicRanges IRanges plotrix S4Vectors SummarizedExperiment]; };
epistasisGA = derive2 { name="epistasisGA"; version="1.6.0"; sha256="1rq1jgd95zamg3fsyj8nbvg95chjaf9d30xlg8d6rr071ya9f03v"; depends=[batchtools BH bigmemory BiocParallel data_table ggplot2 igraph matrixStats qgraph Rcpp RcppArmadillo survival]; };
@ -1471,7 +1474,7 @@ in with self; {
geneRxCluster = derive2 { name="geneRxCluster"; version="1.40.0"; sha256="109ghiv5j33g35d7l71z8s7nc2vb997j5i6vh43nrrygsgc53ywm"; depends=[GenomicRanges IRanges]; };
geneXtendeR = derive2 { name="geneXtendeR"; version="1.30.0"; sha256="06rmxlahnf0xiwvyfl6h9727g8cm24zk6p27j5bb4vln4phb81x7"; depends=[AnnotationDbi BiocStyle data_table dplyr GO_db networkD3 org_Rn_eg_db RColorBrewer rtracklayer SnowballC tm wordcloud]; };
genefilter = derive2 { name="genefilter"; version="1.86.0"; sha256="0jp7jvgzb1bs0p76j9k8lhgliipjnif6bng7hdn5wi744jb5fmpr"; depends=[annotate AnnotationDbi Biobase MatrixGenerics survival]; };
genefu = derive2 { name="genefu"; version="2.36.0"; sha256="032xfs2vp0n0r3sz79fs0v8q28n2sqbnazfwkc3p9dwh4s7nqfwx"; depends=[AIMS amap biomaRt iC10 impute limma mclust survcomp]; };
genefu = derive2 { name="genefu"; version="2.36.0"; sha256="032xfs2vp0n0r3sz79fs0v8q28n2sqbnazfwkc3p9dwh4s7nqfwx"; depends=[AIMS amap biomaRt impute limma mclust survcomp]; };
geneplast = derive2 { name="geneplast"; version="1.30.0"; sha256="1z76dpa7cmzidw3512ynphrrqcqvbrp1bbl8bzcf3jsjdshy7mm7"; depends=[ape data_table igraph snow]; };
geneplotter = derive2 { name="geneplotter"; version="1.82.0"; sha256="19znr3vwp20x84jiwy0im7s6vd8a71yng8w2ji88ffzq0xdkyyjm"; depends=[annotate AnnotationDbi Biobase BiocGenerics lattice RColorBrewer]; };
genoCN = derive2 { name="genoCN"; version="1.56.0"; sha256="1nqxp99g3maxjip9mvpkdm2n6v5vmw7dnkni3nfv2azd12cl9ka1"; depends=[]; };
@ -1507,6 +1510,7 @@ in with self; {
goSTAG = derive2 { name="goSTAG"; version="1.28.0"; sha256="195vdjaxq8xwyz5ib9csk0a1fw6l9pzkpji78l3pbh9p5clw5592"; depends=[AnnotationDbi biomaRt GO_db memoise]; };
goSorensen = derive2 { name="goSorensen"; version="1.6.0"; sha256="1n0i9xmdxnh52lg60klblgi6bzfa910p4ajavir725p84hbqxdjh"; depends=[clusterProfiler GO_db goProfiles org_Hs_eg_db stringr]; };
goTools = derive2 { name="goTools"; version="1.78.0"; sha256="17xpmlsy35a72mbk5c3am85ihgdbwzzaspkb2cfnww9gcnsk6is5"; depends=[AnnotationDbi GO_db]; };
goseq = derive2 { name="goseq"; version="1.56.0"; sha256="0bc7dcpz0agbc42f8agf05amyhpavz55fdp622if5af5dn1ww6pr"; depends=[AnnotationDbi BiasedUrn BiocGenerics geneLenDataBase GO_db mgcv]; };
gpls = derive2 { name="gpls"; version="1.76.0"; sha256="0n2m4himkdzazshiwvxybp5rr1d6jsg60lc5dbsk40grra3w2g4m"; depends=[]; };
gpuMagic = derive2 { name="gpuMagic"; version="1.20.0"; sha256="06ga6xkk95kgnzgy95kzysz8nim9v9aq2s6742hhknjndhy59n28"; depends=[BiocGenerics Deriv DescTools digest pryr Rcpp stringr]; };
granulator = derive2 { name="granulator"; version="1.12.0"; sha256="0757xhxn3156687nz8dksqqs0ifafrdwz0am532pw3xf5hirdz81"; depends=[cowplot dplyr dtangle e1071 epiR ggplot2 ggplotify limSolve magrittr MASS nnls pheatmap purrr rlang tibble tidyr]; };
@ -1564,6 +1568,7 @@ in with self; {
iasva = derive2 { name="iasva"; version="1.22.0"; sha256="14p159ffi41lg56kjc2yafrxd8d0miqnavdnbspaal8l6r4qr10y"; depends=[BiocParallel cluster irlba SummarizedExperiment]; };
ibh = derive2 { name="ibh"; version="1.52.0"; sha256="1xwcvj5zaax3z7c8nnlrmg1bj1wjrrpx5fg5zknhfkv96ycvbk5s"; depends=[simpIntLists]; };
icetea = derive2 { name="icetea"; version="1.22.0"; sha256="0l204ak1br5xhlmp21v4qxc5fzrpg74ylaac63dvvhpkhphl51iz"; depends=[BiocGenerics BiocParallel Biostrings csaw DESeq2 edgeR GenomicAlignments GenomicFeatures GenomicRanges ggplot2 IRanges limma Rsamtools rtracklayer S4Vectors ShortRead SummarizedExperiment TxDb_Dmelanogaster_UCSC_dm6_ensGene VariantAnnotation]; };
ideal = derive2 { name="ideal"; version="1.28.0"; sha256="1fmqawzlg7dzhb6imsq9wjb3i4qr91f6aj4n4akpkrky7djdn3p2"; depends=[AnnotationDbi base64enc BiocParallel DESeq2 dplyr DT GenomicRanges ggplot2 ggrepel GO_db goseq GOstats gplots heatmaply IHW IRanges knitr limma pcaExplorer pheatmap plotly rentrez rintrojs rlang rmarkdown S4Vectors shiny shinyAce shinyBS shinydashboard stringr SummarizedExperiment topGO UpSetR]; };
idiogram = derive2 { name="idiogram"; version="1.80.0"; sha256="0hhgxsc4lk2lpi7ih1z72n4ly8kh8pj9j3w79x7nn0jha5krjv48"; depends=[annotate Biobase plotrix]; };
idpr = derive2 { name="idpr"; version="1.14.0"; sha256="1g6g1265ncwlz4qz3w2v66jimx68pwmlzn8yw94pm242c2ikyn78"; depends=[Biostrings dplyr ggplot2 jsonlite magrittr plyr rlang]; };
idr2d = derive2 { name="idr2d"; version="1.18.0"; sha256="1c1x9nazmapdk820i3k2b4b956zy5ym333y2fjxg9nqfsvq153mn"; depends=[dplyr futile_logger GenomeInfoDb GenomicRanges ggplot2 idr IRanges magrittr reticulate scales stringr]; };
@ -1605,7 +1610,7 @@ in with self; {
lineagespot = derive2 { name="lineagespot"; version="1.8.0"; sha256="0rjf4liq6lr6i3b2a0cn22qc1xisscsvn7zi11vq8wq0ym15pj6c"; depends=[data_table httr MatrixGenerics stringr SummarizedExperiment VariantAnnotation]; };
lionessR = derive2 { name="lionessR"; version="1.18.0"; sha256="1rv9daa45if6nm3yh1sbpnywmdpdi0kmga25pwzfjwv26f9kyd6q"; depends=[S4Vectors SummarizedExperiment]; };
lipidr = derive2 { name="lipidr"; version="2.18.0"; sha256="037xy9ci3h0913df5iy5xnciz26zr9frqfpk8krbx7qfzk4d0rk2"; depends=[data_table dplyr fgsea forcats ggplot2 imputeLCMD limma magrittr rlang ropls S4Vectors SummarizedExperiment tidyr]; };
lisaClust = derive2 { name="lisaClust"; version="1.12.0"; sha256="0sv2x9727nm436czbv6hwpa1psdcf0yl7bzqsfahnpr8bdp04sjy"; depends=[BiocGenerics BiocParallel class concaveman data_table dplyr ggplot2 pheatmap purrr S4Vectors SingleCellExperiment SpatialExperiment spatstat_explore spatstat_geom spatstat_random spicyR SummarizedExperiment tidyr]; };
lisaClust = derive2 { name="lisaClust"; version="1.12.1"; sha256="1yagv5c398kk95c8gyny7ldhh7mpf1yrqp65ijk0xgx5xpl3kcfd"; 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="1.46.0"; sha256="19rplb4ik9jpxqghmglqhv42plbgz01i4pdw7pr063cdc2n3n18g"; depends=[limma pls stemHypoxia]; };
loci2path = derive2 { name="loci2path"; version="1.24.0"; sha256="0igamscdyblh7ymj62qimwr48qfvpqld4ami0m3bnlzkkds6xm2n"; depends=[BiocParallel data_table GenomicRanges pheatmap RColorBrewer S4Vectors wordcloud]; };
logicFS = derive2 { name="logicFS"; version="2.24.0"; sha256="1dbc8zwgixjjcdhy3fgln08c0kycrzbcd46vqjb4l479pdrj2r0l"; depends=[LogicReg mcbiopi survival]; };
@ -1634,7 +1639,7 @@ in with self; {
massiR = derive2 { name="massiR"; version="1.40.0"; sha256="169gpddm1q3brj49sm3sp4ifyby37i41ydxjizwpa9aml90zc0y8"; depends=[Biobase cluster diptest gplots]; };
mastR = derive2 { name="mastR"; version="1.4.0"; sha256="1717hyil3x4c6jqv4zv6fwppwq1lc74kd8hg8z8yj8qqp92093f8"; depends=[AnnotationDbi Biobase dplyr edgeR ggplot2 ggpubr GSEABase limma Matrix msigdb org_Hs_eg_db patchwork SeuratObject SingleCellExperiment SummarizedExperiment tidyr]; };
matchBox = derive2 { name="matchBox"; version="1.46.0"; sha256="015gdqbwdl02mwr7hcymdkz8pvbxjh4qv4agswh3d8qd3mmj04y6"; depends=[]; };
matter = derive2 { name="matter"; version="2.6.1"; sha256="0hzwzjdzl585n82596wd5kmn9wgrmy485pcb44hjcfgy3k58br3n"; depends=[biglm BiocGenerics BiocParallel digest irlba Matrix ProtGenerics]; };
matter = derive2 { name="matter"; version="2.6.2"; sha256="06ql73amrl5zy3ldm4ni3vwv65j1v9fy5s7a2pvwi31w4nwdly6h"; depends=[biglm BiocGenerics BiocParallel digest irlba Matrix ProtGenerics]; };
mbQTL = derive2 { name="mbQTL"; version="1.4.0"; sha256="04ml4rv1hngr8lm9z9pcg7szb1cmla1m1vypwjk9bkkfy879ribf"; depends=[broom dplyr ggplot2 MatrixEQTL metagenomeSeq pheatmap readxl stringr tidyr]; };
mbkmeans = derive2 { name="mbkmeans"; version="1.20.0"; sha256="0fnf6ymbcfchhlcbwpwlcq1jc3lfzh9f8mf76xfy7vrpwngds1fs"; depends=[beachmat benchmarkme BiocParallel ClusterR DelayedArray Matrix Rcpp RcppArmadillo Rhdf5lib S4Vectors SingleCellExperiment SummarizedExperiment]; };
mdp = derive2 { name="mdp"; version="1.24.0"; sha256="08x2ghj5a91rdqq48xjsq4m22qk2ys92jhb6flaqzqgm1s6806lw"; depends=[ggplot2 gridExtra]; };
@ -1706,14 +1711,15 @@ in with self; {
mixOmics = derive2 { name="mixOmics"; version="6.28.0"; sha256="03pdg2hz4wnyigqakb9098ak9ww8fhwypzn006hfad0s042p9wvj"; depends=[BiocParallel corpcor dplyr ellipse ggplot2 ggrepel gridExtra igraph lattice MASS matrixStats rARPACK RColorBrewer reshape2 tidyr]; };
mnem = derive2 { name="mnem"; version="1.20.0"; sha256="0i93fnqpf8m90bkyvgzccj2x4phg9k1wb6k8fs04qsid0b9ksnpd"; depends=[cluster data_table e1071 flexclust ggplot2 graph lattice Linnorm matrixStats naturalsort Rcpp RcppEigen Rgraphviz snowfall tsne wesanderson]; };
moanin = derive2 { name="moanin"; version="1.12.0"; sha256="15agfggzbdgpx974yvixh8c8mv8wklg6zfzzr7ywpv2cixxazhwq"; depends=[ClusterR edgeR limma MASS matrixStats NMI reshape2 S4Vectors SummarizedExperiment topGO viridis zoo]; };
mobileRNA = derive2 { name="mobileRNA"; version="1.0.1"; sha256="1rp6y71rnqxpjmjfa4mx1l7ndb94l7443xvjzkvkh8axizwlml6y"; depends=[BiocGenerics bioseq Biostrings data_table DESeq2 dplyr edgeR GenomeInfoDb GenomicRanges ggplot2 ggrepel IRanges pheatmap progress RColorBrewer reticulate rlang rtracklayer S4Vectors scales SimDesign SummarizedExperiment tidyr tidyselect]; };
mobileRNA = derive2 { name="mobileRNA"; version="1.0.11"; sha256="10p37qr8wz6chh44fh1nri2db5qqghbbzbpjm02safxdx7h88081"; depends=[BiocGenerics bioseq Biostrings data_table DESeq2 dplyr edgeR GenomeInfoDb GenomicRanges ggplot2 ggrepel IRanges pheatmap progress RColorBrewer reticulate rlang rtracklayer S4Vectors scales SimDesign SummarizedExperiment tidyr tidyselect]; };
mogsa = derive2 { name="mogsa"; version="1.38.0"; sha256="01hr97j5i20qwpck6nfr79wx31y7igz1wzr2m1zdivggb4jg94x7"; depends=[Biobase BiocGenerics cluster corpcor genefilter gplots graphite GSEABase svd]; };
monaLisa = derive2 { name="monaLisa"; version="1.10.0"; sha256="0znan1yh35mxrjn6x5xz2g5pl0dhh0nklyx8rbsn09hn1khb8y5l"; depends=[BiocGenerics BiocParallel Biostrings BSgenome circlize ComplexHeatmap GenomeInfoDb GenomicRanges glmnet IRanges RSQLite S4Vectors stabs SummarizedExperiment TFBSTools vioplot XVector]; };
monocle = derive2 { name="monocle"; version="2.32.0"; sha256="0b09mf9fph0mb0zing0prc757d223858q9lj4j3kfpfjpd3jffai"; depends=[Biobase BiocGenerics biocViews cluster combinat DDRTree dplyr fastICA ggplot2 HSMMSingleCell igraph irlba leidenbase limma MASS Matrix matrixStats pheatmap plyr proxy RANN Rcpp reshape2 Rtsne slam stringr tibble VGAM viridis]; };
mosaics = derive2 { name="mosaics"; version="2.42.0"; sha256="000bwz1z8nwzgyaz69z6krr4ksggpsq48ni9rzl25m1bc27skldj"; depends=[GenomeInfoDb GenomicAlignments GenomicRanges IRanges lattice MASS Rcpp Rsamtools S4Vectors]; };
mosbi = derive2 { name="mosbi"; version="1.10.0"; sha256="0kvwsiwqvsphgjcflr1zjhp91k867bqg6x6gj72kl6x9an3rxpri"; depends=[akmbiclust BH biclust fabia igraph isa2 QUBIC RColorBrewer Rcpp RcppParallel xml2]; };
mosdef = derive2 { name="mosdef"; version="1.0.0"; sha256="14zv9mgiqcj2s34hg8wfdij1gss324rkq42clg8f3ancambj74vp"; depends=[AnnotationDbi clusterProfiler DESeq2 DT ggforce ggplot2 ggrepel GO_db goseq htmltools RColorBrewer rlang S4Vectors scales SummarizedExperiment topGO]; };
motifStack = derive2 { name="motifStack"; version="1.48.0"; sha256="15v4z1a0kg4ic411aprzc9b7i2l6c456sfj3jaxy95anw3j3iskj"; depends=[ade4 Biostrings ggplot2 htmlwidgets TFBSTools XML]; };
motifTestR = derive2 { name="motifTestR"; version="1.0.0"; sha256="18syzq8abxbfa6wc1fm221rkflhlh7h8v1r8q44y2x7zlm8ijlkc"; depends=[Biostrings GenomeInfoDb GenomicRanges ggplot2 harmonicmeanp IRanges matrixStats patchwork rlang S4Vectors universalmotif]; };
motifTestR = derive2 { name="motifTestR"; version="1.0.3"; sha256="19m8y69cd1x79cqwgwf6360mv7kn0a2gv3lphy2i60p6vlq99s8j"; depends=[Biostrings GenomeInfoDb GenomicRanges ggplot2 harmonicmeanp IRanges matrixStats patchwork rlang S4Vectors universalmotif]; };
motifbreakR = derive2 { name="motifbreakR"; version="2.18.0"; sha256="1mxs83l8yrbcx353h0wpc0lczn1jc0y5vg59y9g9dabk41csib47"; depends=[BiocGenerics BiocParallel Biostrings BSgenome GenomeInfoDb GenomicRanges Gviz IRanges matrixStats MotifDb motifStack pwalign rtracklayer S4Vectors stringr SummarizedExperiment TFMPvalue VariantAnnotation]; };
motifcounter = derive2 { name="motifcounter"; version="1.28.0"; sha256="1h6wbqn2xbj5ggx0sgp09cvrkcafq7i70mbskg2y9l9nryb38g2z"; depends=[Biostrings]; };
motifmatchr = derive2 { name="motifmatchr"; version="1.26.0"; sha256="1wpvdg5x51cbzpqa4s2s0zl9h7fsrsp87mxxlhxs65zx6yyfj2xl"; depends=[Biostrings BSgenome GenomeInfoDb GenomicRanges IRanges Matrix Rcpp RcppArmadillo Rsamtools S4Vectors SummarizedExperiment TFBSTools]; };
@ -1770,7 +1776,7 @@ in with self; {
occugene = derive2 { name="occugene"; version="1.64.0"; sha256="01dgpbz3w5bbbhiz67fripxw1pwdd1iinnywvm9xgzjkdhr3g18y"; depends=[]; };
octad = derive2 { name="octad"; version="1.6.0"; sha256="1nlad40c9mzs74zrc82smmmyknw4dr88c6zm0ywm62v0wb8l22n7"; depends=[AnnotationHub Biobase data_table DESeq2 dplyr EDASeq edgeR ExperimentHub foreach ggplot2 GSVA htmlwidgets httr limma magrittr octad_db plotly qpdf reshape2 Rfast rhdf5 RUVSeq S4Vectors]; };
odseq = derive2 { name="odseq"; version="1.32.0"; sha256="03bhlarifh5r13ii7a5kd6gj9w0zdgjz9p89pj0lhgx2lglh2nm8"; depends=[kebabs mclust msa]; };
oligo = derive2 { name="oligo"; version="1.68.0"; sha256="0mv031fsy1g3k0brxx8z7d1ryg0z2nxihrs22n6ln2jk240lkyfx"; depends=[affxparser affyio Biobase BiocGenerics Biostrings DBI ff oligoClasses preprocessCore RSQLite zlibbioc]; };
oligo = derive2 { name="oligo"; version="1.68.2"; sha256="0ch6b4rg5v6fj0fgniqiigx1gnnqgwji90bxqngllman388bx867"; depends=[affxparser affyio Biobase BiocGenerics Biostrings DBI ff oligoClasses preprocessCore RSQLite zlibbioc]; };
oligoClasses = derive2 { name="oligoClasses"; version="1.66.0"; sha256="15icfcmpwrnjpyahc4v168fpcbsml6x7h4drmsyh9l8d1284yb4n"; depends=[affyio Biobase BiocGenerics BiocManager Biostrings DBI ff foreach GenomicRanges IRanges RSQLite S4Vectors SummarizedExperiment]; };
omada = derive2 { name="omada"; version="1.6.0"; sha256="1by6im4frl724yif9pjgcmp016hahj5xj35h1zqa4k5g8nw54f9s"; depends=[clValid diceR dplyr fpc genieclust ggplot2 glmnet kernlab pdfCluster Rcpp reshape]; };
omicRexposome = derive2 { name="omicRexposome"; version="1.26.0"; sha256="0p3x3pp3337nvmqqssrbfh6zn2fp260ss8wjc2c90b0gr4c4h6wc"; depends=[Biobase ggplot2 ggrepel gridExtra isva limma MultiDataSet omicade4 PMA rexposome SmartSVA stringr SummarizedExperiment sva]; };
@ -1812,6 +1818,7 @@ in with self; {
pathlinkR = derive2 { name="pathlinkR"; version="1.0.0"; sha256="19i840an94hpyqxz4c4piqy322ynxzf48cxbmxvf5jylxdqjnzf2"; depends=[circlize clusterProfiler ComplexHeatmap dplyr ggforce ggplot2 ggpubr ggraph ggrepel igraph purrr sigora stringr tibble tidygraph tidyr vegan visNetwork]; };
pathview = derive2 { name="pathview"; version="1.44.0"; sha256="1papw23dhhkqmm864dc3xm028xm0ywc6sjcm7xk93f2j7yj65x0v"; depends=[AnnotationDbi graph KEGGgraph KEGGREST org_Hs_eg_db png Rgraphviz XML]; };
pathwayPCA = derive2 { name="pathwayPCA"; version="1.20.0"; sha256="055jqyzi6lq056ibdyzxy5mzcs5f93im2fbiz73a33bqndpc9s5i"; depends=[lars survival]; };
paxtoolsr = derive2 { name="paxtoolsr"; version="1.38.0"; sha256="0m3r8ynqkhksgj0d3si3wcnk5a801g1qklin8zm81cr1nlfx67gw"; depends=[httr igraph jsonlite plyr R_utils rappdirs readr rJava rjson XML]; };
pcaExplorer = derive2 { name="pcaExplorer"; version="2.30.0"; sha256="1szl2gyhw55ad4phcb7qn14amjb6xg65l3p4hnjzp6rda2cy9437"; depends=[AnnotationDbi base64enc biomaRt DESeq2 DT genefilter GenomicRanges ggplot2 ggrepel GO_db GOstats heatmaply IRanges knitr limma NMF pheatmap plotly plyr rmarkdown S4Vectors scales shiny shinyAce shinyBS shinydashboard SummarizedExperiment threejs tidyr topGO]; };
pcaMethods = derive2 { name="pcaMethods"; version="1.96.0"; sha256="1hrq0xmpr1l95hyi6ls9r86ahwf2rcbvr8m7cpg6ra0gsfyn4mpi"; depends=[Biobase BiocGenerics MASS Rcpp]; };
pcxn = derive2 { name="pcxn"; version="2.26.0"; sha256="13gahdsvz7ss3chcvqmdyrnw31rcgiplqg7awrn930drwljlimqk"; depends=[pcxnData pheatmap]; };
@ -1843,7 +1850,7 @@ in with self; {
plgem = derive2 { name="plgem"; version="1.76.0"; sha256="0my4jpxw3xy9n40cqvdaz6ay7gpwshn2iqxr43knrk0ckpyxx2cr"; depends=[Biobase MASS]; };
plier = derive2 { name="plier"; version="1.74.0"; sha256="0svk8p4h212l3igfmrxhqi90xz74jicr5y780556k9bcj3jwqg5c"; depends=[affy Biobase]; };
plotGrouper = derive2 { name="plotGrouper"; version="1.22.0"; sha256="169786jrqbcf8qhysar22cb5am2zh6j7w601k9784b4ywhxh3ac0"; depends=[colourpicker dplyr egg ggplot2 ggpubr gridExtra gtable Hmisc magrittr readr readxl rlang scales shiny shinythemes stringr tibble tidyr]; };
plotgardener = derive2 { name="plotgardener"; version="1.10.0"; sha256="1bpxszy3i4fbp2wz0swy6zwszd531ahpyfnh25d63n8qd35489wa"; depends=[curl data_table dplyr GenomeInfoDb GenomicRanges ggplotify IRanges plyranges purrr RColorBrewer Rcpp rlang strawr withr]; };
plotgardener = derive2 { name="plotgardener"; version="1.10.1"; sha256="1pcjc4an5pspafb9pvmia73g8cdp6n2paz2m952p1xnwsp9ijsi7"; depends=[curl data_table dplyr GenomeInfoDb GenomicRanges ggplotify IRanges plyranges purrr RColorBrewer Rcpp rlang strawr withr]; };
plyinteractions = derive2 { name="plyinteractions"; version="1.2.0"; sha256="095sb616r5xwcbqsgw4b7kiywl6lbwp6rbs80qymglpqkbywwp7j"; depends=[BiocGenerics dplyr GenomeInfoDb GenomicRanges InteractionSet IRanges plyranges rlang S4Vectors tibble tidyselect]; };
plyranges = derive2 { name="plyranges"; version="1.24.0"; sha256="0rh5l6bd80nhffqpnnc2c00mvp8p32ykld05h94c3y8c9mvmsl58"; depends=[BiocGenerics dplyr GenomeInfoDb GenomicAlignments GenomicRanges IRanges magrittr rlang Rsamtools rtracklayer S4Vectors tidyselect]; };
pmm = derive2 { name="pmm"; version="1.36.0"; sha256="1qsv7mrz1w5msxkiqp1rvxy5cgfjkwm432c12rr3gm4z3jy1ma5h"; depends=[lme4]; };
@ -1933,6 +1940,7 @@ in with self; {
rfPred = derive2 { name="rfPred"; version="1.42.0"; sha256="02clazsix7n4nnz1kn7hkk48fggxp2bqf97xbzngnljskvlhnakb"; depends=[data_table GenomeInfoDb GenomicRanges IRanges Rsamtools]; };
rfaRm = derive2 { name="rfaRm"; version="1.16.0"; sha256="1c8kpcbwkz33cbc8xqfd5cqj1n979a9ijbj06nfgylkm71ma1682"; depends=[Biostrings data_table httr IRanges jsonlite magick rsvg rvest S4Vectors stringi xml2]; };
rgoslin = derive2 { name="rgoslin"; version="1.8.0"; sha256="0saxw5kppcw0hwjykgzx8873izbl509hq1ga8w9qg2c5zx5xahk9"; depends=[dplyr Rcpp]; };
rgsepd = derive2 { name="rgsepd"; version="1.36.0"; sha256="18r2naxir299k0gcd9j3a5rvdma590m06v38j8wiligsgw5cmkfg"; depends=[AnnotationDbi biomaRt DESeq2 GO_db goseq gplots org_Hs_eg_db SummarizedExperiment]; };
rhdf5 = derive2 { name="rhdf5"; version="2.48.0"; sha256="086bnwzmlwq3z9a4kb1rnzb2wnchhi4gvzpijhladgd83nqyb0wn"; depends=[rhdf5filters Rhdf5lib]; };
rhdf5client = derive2 { name="rhdf5client"; version="1.26.0"; sha256="17c8r361za3760lkik2b88c3m8zska33qam2iwbl5hw9yhkrl6ck"; depends=[data_table DelayedArray httr rjson]; };
rhdf5filters = derive2 { name="rhdf5filters"; version="1.16.0"; sha256="0fsfp34pfb5k030j7nfx9b9vsil02y85sv1dd1y0bfdxchi4bw8x"; depends=[Rhdf5lib]; };
@ -2061,7 +2069,7 @@ in with self; {
skewr = derive2 { name="skewr"; version="1.36.0"; sha256="1hh0519pqv6lq21plph7sy88918np12g7aw542sfblm81ma4p4qv"; depends=[IlluminaHumanMethylation450kmanifest methylumi minfi mixsmsn RColorBrewer S4Vectors wateRmelon]; };
slalom = derive2 { name="slalom"; version="1.26.0"; sha256="0km062qb7k7g18zz03nr6m7nigzpbxkasgirc4igslz4sfcldd9x"; depends=[BH ggplot2 GSEABase Rcpp RcppArmadillo rsvd SingleCellExperiment SummarizedExperiment]; };
slingshot = derive2 { name="slingshot"; version="2.12.0"; sha256="055dylajbn94khi0829qhxx0lbn1pvh30xw09gjn1jvxsgzj49nc"; depends=[igraph matrixStats princurve S4Vectors SingleCellExperiment SummarizedExperiment TrajectoryUtils]; };
smartid = derive2 { name="smartid"; version="1.0.1"; sha256="15q4x3smvz6kn12960vk1bqbap288kbww141glh77lfdzwvlmpd9"; depends=[dplyr ggplot2 Matrix mclust mixtools sparseMatrixStats SummarizedExperiment tidyr]; };
smartid = derive2 { name="smartid"; version="1.0.2"; sha256="1bm8g8n3xifc2dg1d9vpw79vpwssa9q6ssvzyf77gp24zp2r734i"; depends=[dplyr ggplot2 Matrix mclust mixtools sparseMatrixStats SummarizedExperiment tidyr]; };
smoothclust = derive2 { name="smoothclust"; version="1.0.0"; sha256="17mcfjxsgdvignrx576v97iwapmkfc4my8pvm6b2y1w7pibilx65"; depends=[sparseMatrixStats SpatialExperiment spdep SummarizedExperiment]; };
snapcount = derive2 { name="snapcount"; version="1.16.0"; sha256="1hjd6xdwgz2qal6scpldwpdqlrbgap45bq2h599df6hgvrdym3l7"; depends=[assertthat data_table GenomicRanges httr IRanges jsonlite magrittr Matrix purrr R6 rlang stringr SummarizedExperiment]; };
snifter = derive2 { name="snifter"; version="1.14.0"; sha256="1rmg6dq7sm7aisjrli8ya1wx2b0y0vngf5zksy1x77v6c5mk4b72"; depends=[assertthat basilisk irlba reticulate]; };
@ -2202,7 +2210,7 @@ in with self; {
wiggleplotr = derive2 { name="wiggleplotr"; version="1.28.0"; sha256="1px7rgvaj6kks6fp7yqsqjwy4knlzgllzxsiimv8nikmbd57dmi0"; depends=[assertthat cowplot dplyr GenomeInfoDb GenomicRanges ggplot2 IRanges purrr rtracklayer S4Vectors]; };
wpm = derive2 { name="wpm"; version="1.14.0"; sha256="1623q58fjxnx1632fn5c5rhx0zpglbjpp7zqp15f2gch01ac0xdy"; depends=[Biobase cli config dplyr DT ggplot2 golem logging RColorBrewer rlang shiny shinycustomloader shinydashboard shinyWidgets stringr SummarizedExperiment]; };
wppi = derive2 { name="wppi"; version="1.12.0"; sha256="1mvr5bpsng87yl1bhd22h45830vw3sla1ysnr29px13if2q5ylmy"; depends=[dplyr igraph logger magrittr Matrix OmnipathR progress purrr RCurl rlang tibble tidyr]; };
xcms = derive2 { name="xcms"; version="4.2.1"; sha256="1q3nz59572s10raaxr90nwcj69dd1an034fpdbczlbjbskzzns4f"; depends=[Biobase BiocGenerics BiocParallel IRanges jsonlite lattice MassSpecWavelet MetaboCoreUtils MsCoreUtils MsExperiment MsFeatures MSnbase mzR progress ProtGenerics RColorBrewer S4Vectors Spectra SummarizedExperiment]; };
xcms = derive2 { name="xcms"; version="4.2.2"; sha256="1zk9l4ll3047fj0rngvjka2hkg2by26n2h3xm1iyvfiw5068y74y"; depends=[Biobase BiocGenerics BiocParallel IRanges jsonlite lattice MassSpecWavelet MetaboCoreUtils MsCoreUtils MsExperiment MsFeatures MSnbase mzR progress ProtGenerics RColorBrewer S4Vectors Spectra SummarizedExperiment]; };
xcore = derive2 { name="xcore"; version="1.8.0"; sha256="04156svl1cjbhy51d7fbgdilp832wfifg37yr9civ829iyi79fha"; depends=[DelayedArray edgeR foreach GenomicRanges glmnet IRanges iterators magrittr Matrix MultiAssayExperiment S4Vectors]; };
xmapbridge = derive2 { name="xmapbridge"; version="1.62.0"; sha256="0laahd3v5m313q1iq259aikgqf7zlmpxyxhws2pr7vg97g37bbhs"; depends=[]; };
yamss = derive2 { name="yamss"; version="1.30.0"; sha256="0l9wqijwlq1gwybj2fy6jwgq6ja1mvx8yfdv174g5mjflx8nmc06"; depends=[BiocGenerics data_table EBImage IRanges limma Matrix mzR S4Vectors SummarizedExperiment]; };
@ -2239,7 +2247,6 @@ in with self; {
CancerSubtypes = derive2 { name="CancerSubtypes"; version="1.26.0"; sha256="06lw7b43fwh554870w71i676q6gm6kx53580cgg17a7prdjndkmr"; depends=[cluster ConsensusClusterPlus impute limma NMF sigclust survival]; broken = true; };
CellaRepertorium = derive2 { name="CellaRepertorium"; version="1.12.0"; sha256="0k9sxh0b9g2841zpkbmcc65v0kfyv1i6sxzdmbr49nzzm27xlbh2"; depends=[BiocGenerics Biostrings dplyr forcats generics glue Matrix progress purrr Rcpp reshape2 rlang S4Vectors stringr tibble tidyr]; broken = true; };
Cepo = derive2 { name="Cepo"; version="1.8.0"; sha256="0s1zra4msgbp37r5lp0zs9j2aq054rcmrmhwi3liwp4wkvjbshw8"; depends=[BiocParallel DelayedArray DelayedMatrixStats dplyr ggplot2 GSEABase HDF5Array patchwork reshape2 rlang S4Vectors SingleCellExperiment SummarizedExperiment]; broken = true; };
ChAMP = derive2 { name="ChAMP"; version="2.32.0"; sha256="1gdcdx34bxffd6ch354qx7yjngx3lj9chv5frwjyk56jq12vjjk7"; 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]; broken = true; };
ChIC = derive2 { name="ChIC"; version="1.19.0"; sha256="0zbmhixxn3skn8csz93fyyfamz1n3gzjzb2caw8ybi2cysgzz5ys"; depends=[BiocGenerics caret caTools ChIC_data genomeIntervals GenomicRanges IRanges progress randomForest Rsamtools S4Vectors]; broken = true; };
Clonality = derive2 { name="Clonality"; version="1.47.0"; sha256="0yxwwc0sl3impvzr0bmjmdn65z6qx6lf5pwik2p8wxxgaybvff9r"; depends=[DNAcopy]; broken = true; };
CoRegNet = derive2 { name="CoRegNet"; version="1.38.0"; sha256="19df43l35dkf36dhq8fx8a9gm1grxymrmpcix0b4qmxrzwjp0s8k"; depends=[arules igraph shiny]; broken = true; };
@ -2331,7 +2338,6 @@ in with self; {
SISPA = derive2 { name="SISPA"; version="1.30.0"; sha256="0glqk2p06brw9a9prccil02z82nhq2izh2sgfrlmi1kpf8mgszl3"; depends=[changepoint data_table genefilter ggplot2 GSVA plyr]; broken = true; };
SLGI = derive2 { name="SLGI"; version="1.54.0"; sha256="03jwdq4k44rys3f773c6l985a6v1bacbdghw97p0qpwspmzra8rs"; depends=[AnnotationDbi Biobase BiocGenerics GO_db lattice]; broken = true; };
SMAP = derive2 { name="SMAP"; version="1.66.0"; sha256="0m6jvb3jpnk36cv8grj1s3af6nm9xnn3x0mxkrwfbpgzvcn5735n"; depends=[]; broken = true; };
SMITE = derive2 { name="SMITE"; version="1.30.0"; sha256="0hz0wjfw43l1s3hdmwvpy3623ps8alhblc1lb06dnx0pa7r3gljd"; depends=[AnnotationDbi Biobase BioNet geneLenDataBase GenomicRanges ggplot2 goseq Hmisc igraph IRanges KEGGREST org_Hs_eg_db plyr reactome_db S4Vectors scales]; broken = true; };
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]; broken = true; };
SQUADD = derive2 { name="SQUADD"; version="1.52.0"; sha256="0vg7mhx2aldk53jdgy4k8yk3jyjwklmp13mxch7cxinr8bzbyjh6"; depends=[RColorBrewer]; broken = true; };
STAN = derive2 { name="STAN"; version="2.26.2"; sha256="0dd4hb2iabvnr6v0ys4jslj7611z1hii8hxkdvwrjbz4nn678wkv"; depends=[BiocGenerics GenomeInfoDb GenomicRanges Gviz IRanges poilog Rsolnp S4Vectors]; broken = true; };
@ -2395,10 +2401,8 @@ in with self; {
genbankr = derive2 { name="genbankr"; version="1.27.0"; sha256="0fv87cf2y10ijlb0g1x9g9wh95qyljqb1c7k1ihbnjcg36xkh8lc"; depends=[Biobase BiocGenerics Biostrings GenomeInfoDb GenomicFeatures GenomicRanges IRanges rtracklayer S4Vectors VariantAnnotation]; broken = true; };
genotypeeval = derive2 { name="genotypeeval"; version="1.30.0"; sha256="0mi1d86i4v8gafwszy978n61s5pszrsmbh1in4nggdqwvwnvkqnl"; depends=[BiocGenerics BiocParallel GenomeInfoDb GenomicRanges ggplot2 IRanges rtracklayer VariantAnnotation]; broken = true; };
genphen = derive2 { name="genphen"; version="1.24.0"; sha256="1m60qagcxviix4zjzfhvrwchbjq2clss6mivb8q07bcq369yw1b8"; depends=[Biostrings doParallel e1071 foreach ranger Rcpp rPref rstan]; broken = true; };
goseq = derive2 { name="goseq"; version="1.54.0"; sha256="0waw5hhxh8yab8fqw9gnd3l39s6wkmp8690rhs4llarpqz6ssrhk"; depends=[AnnotationDbi BiasedUrn BiocGenerics geneLenDataBase GO_db mgcv]; broken = true; };
gpart = derive2 { name="gpart"; version="1.13.0"; sha256="1518wjkaw22ckgpwl6si83bhijvib0r0kgs9s4das41f0ygi92sd"; depends=[AnnotationDbi biomaRt data_table GenomicRanges Homo_sapiens igraph IRanges OrganismDbi Rcpp TxDb_Hsapiens_UCSC_hg38_knownGene]; broken = true; };
gprege = derive2 { name="gprege"; version="1.39.0"; sha256="12yjyb7a7jc86hdi3a3cavqxfzkhmds1m2vigzw5ihhx6028pa78"; depends=[]; broken = true; };
ideal = derive2 { name="ideal"; version="1.26.0"; sha256="0k1wxfww3dgfpfllpb1xxn1yjwmrkwf907njg9l85gm997smvdf9"; depends=[AnnotationDbi base64enc BiocParallel DESeq2 dplyr DT GenomicRanges ggplot2 ggrepel GO_db goseq GOstats gplots heatmaply IHW IRanges knitr limma pcaExplorer pheatmap plotly rentrez rintrojs rlang rmarkdown S4Vectors shiny shinyAce shinyBS shinydashboard stringr SummarizedExperiment topGO UpSetR]; broken = true; };
imageHTS = derive2 { name="imageHTS"; version="1.48.0"; sha256="124pksw08b88bj7l8pckzvgk6sf54d633cnbq2r5il7a09i4caim"; depends=[Biobase cellHTS2 e1071 EBImage hwriter vsn]; broken = true; };
inveRsion = derive2 { name="inveRsion"; version="1.43.0"; sha256="0h2q10xf4x22hy7780w4pvq488921wzjngly8qcc97sa8iacssk3"; depends=[haplo_stats]; broken = true; };
iterClust = derive2 { name="iterClust"; version="1.24.0"; sha256="0k2hcc7g4ynd9jrk8f286y6gwc4bfs4bnfs8qpj2i8zamwdaldng"; depends=[Biobase cluster]; broken = true; };
@ -2425,7 +2429,6 @@ in with self; {
nondetects = derive2 { name="nondetects"; version="2.32.0"; sha256="0302mg5pbvbzp9rhm6wg4lfa7c7lkndysx35x8b1zskc4b1v76cv"; depends=[arm Biobase HTqPCR limma mvtnorm]; broken = true; };
oneSENSE = derive2 { name="oneSENSE"; version="1.20.0"; sha256="1lzb8i3frv3va2q28glwnjwszrynhky5y8fx10q4h52p2wqgc4v3"; depends=[flowCore gplots plotly Rtsne scatterplot3d shiny shinyFiles webshot]; broken = true; };
pathVar = derive2 { name="pathVar"; version="1.30.0"; sha256="1q0m4yb4jvi61f3hl7mpbnl9y0y4pqhspi1gn3wp5lf86j8c40jp"; depends=[data_table EMT ggplot2 gridExtra Matching mclust]; broken = true; };
paxtoolsr = derive2 { name="paxtoolsr"; version="1.36.0"; sha256="07rkyn3i6v98lkjz13la0x1g81zhnyyr44jdid5c2dydlfpchl7h"; depends=[httr igraph jsonlite plyr R_utils rappdirs readr rJava rjson XML]; broken = true; };
perturbatr = derive2 { name="perturbatr"; version="1.13.0"; sha256="0ssk8cr42hibn917s2z2nzcdan54c7xiydypbi8f3g4w68q4ly31"; depends=[assertthat diffusr doParallel dplyr foreach formula_tools ggplot2 igraph lazyeval lme4 magrittr rlang scales tibble tidyr]; broken = true; };
phemd = derive2 { name="phemd"; version="1.18.0"; sha256="174jp26insq2mwf9yw9bls4i9b2a8vccfkrg2h1dzvyyk513bi83"; depends=[Biobase BiocGenerics cluster cowplot destiny ggplot2 igraph maptree monocle phateR pheatmap pracma RANN RColorBrewer reticulate Rtsne S4Vectors scatterplot3d Seurat SingleCellExperiment SummarizedExperiment transport VGAM]; broken = true; };
pkgDepTools = derive2 { name="pkgDepTools"; version="1.63.0"; sha256="10q0z1ps073py82zqii4sfdhnpvcyj4sx1yx3lzy5c41l8py6lag"; depends=[graph RBGL]; broken = true; };
@ -2440,7 +2443,6 @@ in with self; {
qrqc = derive2 { name="qrqc"; version="1.52.0"; sha256="0411477y7nazlwbz3pfszr1wfas6qd0g0iz0p9pmq16dw8pzkgg6"; depends=[Biostrings biovizBase brew ggplot2 plyr reshape Rhtslib testthat xtable]; broken = true; };
rama = derive2 { name="rama"; version="1.72.0"; sha256="0i6crxnzhwxnc55xh2rv36jfwh4bd30alw1f05ixdrxwqwsslbpy"; depends=[]; broken = true; };
restfulSE = derive2 { name="restfulSE"; version="1.24.0"; sha256="0i40yfvynxy34jfkvzyvjwvxf89zi4pvy9m9i0bk93l17gyhnjyl"; depends=[AnnotationDbi AnnotationHub bigrquery Biobase DBI DelayedArray dplyr ExperimentHub GO_db magrittr reshape2 rhdf5client rlang S4Vectors SummarizedExperiment]; broken = true; };
rgsepd = derive2 { name="rgsepd"; version="1.34.0"; sha256="1g1h66hbb29hsvjzdyg4s84ihifpqjw0xqm1rrcaqd5l60n8mx4j"; depends=[AnnotationDbi biomaRt DESeq2 GO_db goseq gplots org_Hs_eg_db SummarizedExperiment]; broken = true; };
rqt = derive2 { name="rqt"; version="1.28.0"; sha256="02yvwp68c0xx1wa41hfwmq5zjskqk3jg6z1hvivi6x3l5g2xfwah"; depends=[car CompQuadForm glmnet Matrix metap pls ropls RUnit SummarizedExperiment]; broken = true; };
savR = derive2 { name="savR"; version="1.37.0"; sha256="13wiw7isdmpwhynxjrhimy9yglcz1108k7nwa98vq9czq49zpada"; depends=[ggplot2 gridExtra reshape2 scales XML]; broken = true; };
scAlign = derive2 { name="scAlign"; version="1.12.0"; sha256="1mlhxwsfrmhysa5mcyx7vf2jn49snf41yb7xqmyi40wilj9h8qlb"; depends=[FNN ggplot2 irlba purrr Rtsne Seurat SingleCellExperiment tensorflow]; broken = true; };

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pkgs/development/r-modules/cran-packages.nix generated
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