rPackages: CRAN and BioC update

4 files changed, 3321 insertions, 2827 deletions

diff --git a/pkgs/development/r-modules/bioc-annotation-packages.nix b/pkgs/development/r-modules/bioc-annotation-packages.nix
index 7d47727ed413..096c0f81e572 100644
--- a/pkgs/development/r-modules/bioc-annotation-packages.nix
+++ b/pkgs/development/r-modules/bioc-annotation-packages.nix
@@ -76,10 +76,11 @@ in with self; {
   BSgenome_Hsapiens_UCSC_hg18_masked = derive2 { name="BSgenome.Hsapiens.UCSC.hg18.masked"; version="1.3.99"; sha256="031sr3y95c32igk3lrrsafdm9i1zprjran8gak06arqc0hvzbfk0"; depends=[BSgenome BSgenome_Hsapiens_UCSC_hg18]; };
   BSgenome_Hsapiens_UCSC_hg19 = derive2 { name="BSgenome.Hsapiens.UCSC.hg19"; version="1.4.3"; sha256="06lx7q7i52lg3vkjkqy492z9ianzgi4nhs9m1jrxjjb4hgbnbyjv"; depends=[BSgenome]; };
   BSgenome_Hsapiens_UCSC_hg19_masked = derive2 { name="BSgenome.Hsapiens.UCSC.hg19.masked"; version="1.3.993"; sha256="19533ihgad67bzhavycv6z708012ylz9cw1qdfmk2b7ikf3kiaz9"; depends=[BSgenome BSgenome_Hsapiens_UCSC_hg19]; };
-  BSgenome_Hsapiens_UCSC_hg38 = derive2 { name="BSgenome.Hsapiens.UCSC.hg38"; version="1.4.4"; sha256="03xmh6q99nqjxz29m6j0ymxlk22jq0nlvpf4a2yhg3hgnxqkakh2"; depends=[BSgenome]; };
+  BSgenome_Hsapiens_UCSC_hg38 = derive2 { name="BSgenome.Hsapiens.UCSC.hg38"; version="1.4.5"; sha256="0lp94r9dsx8sl1ifysavgjf4aamhjc4n71zif5jyfnwmzpj7g4ml"; depends=[BSgenome GenomeInfoDb]; };
   BSgenome_Hsapiens_UCSC_hg38_dbSNP151_major = derive2 { name="BSgenome.Hsapiens.UCSC.hg38.dbSNP151.major"; version="0.0.9999"; sha256="0290fk7jvlcb1mh6nlyqagqskfh0dvaysj1d6s15bgygnlm3r726"; depends=[BSgenome]; };
   BSgenome_Hsapiens_UCSC_hg38_dbSNP151_minor = derive2 { name="BSgenome.Hsapiens.UCSC.hg38.dbSNP151.minor"; version="0.0.9999"; sha256="1xw8vckhsak35r942yyvlrpbhb2w4vzah8wfgmn3vyj1zklk3913"; depends=[BSgenome]; };
-  BSgenome_Hsapiens_UCSC_hg38_masked = derive2 { name="BSgenome.Hsapiens.UCSC.hg38.masked"; version="1.4.4"; sha256="0ac5c265pgq1yzyp655ix0awdszzxf3mhrp0qsfsb73msqb2s99n"; depends=[BSgenome BSgenome_Hsapiens_UCSC_hg38]; };
+  BSgenome_Hsapiens_UCSC_hg38_masked = derive2 { name="BSgenome.Hsapiens.UCSC.hg38.masked"; version="1.4.5"; sha256="0j71hdxqvvc0s8mc6jp6zk502mrf095qazj95yzzb4rm6sjvd20m"; depends=[BSgenome BSgenome_Hsapiens_UCSC_hg38 GenomeInfoDb]; };
+  BSgenome_Hsapiens_UCSC_hs1 = derive2 { name="BSgenome.Hsapiens.UCSC.hs1"; version="1.4.4"; sha256="1y5rxlms9fj20fz32l56i5j1c4fzly5zzvlxz01fs46qimnfb3ms"; depends=[BSgenome]; };
   BSgenome_Mdomestica_UCSC_monDom5 = derive2 { name="BSgenome.Mdomestica.UCSC.monDom5"; version="1.4.2"; sha256="16kzb66kjpmf9j92pwh98ah5rhrnfyzdpr0rk659zham6dzga9ck"; depends=[BSgenome]; };
   BSgenome_Mfascicularis_NCBI_5_0 = derive2 { name="BSgenome.Mfascicularis.NCBI.5.0"; version="1.4.2"; sha256="1lrdj7aibx4i60hpbaqgk3qir9zjs67mxdgp5jmgmw7gf2nwyn3x"; depends=[BSgenome]; };
   BSgenome_Mfascicularis_NCBI_6_0 = derive2 { name="BSgenome.Mfascicularis.NCBI.6.0"; version="1.5.0"; sha256="0zl73jkg56jrvqyqvp67jx63dl8li6pypkgn1dqj959qzdzc57j0"; depends=[BSgenome]; };
@@ -125,7 +126,7 @@ in with self; {
   BSgenome_Vvinifera_URGI_IGGP12Xv0 = derive2 { name="BSgenome.Vvinifera.URGI.IGGP12Xv0"; version="0.1"; sha256="1m8mqkiqs7291hccb8pfyf2yxpky45qr6j3d9wkvp9x3ra3h0yxf"; depends=[BSgenome]; };
   BSgenome_Vvinifera_URGI_IGGP12Xv2 = derive2 { name="BSgenome.Vvinifera.URGI.IGGP12Xv2"; version="0.1"; sha256="1saavsi75gw33jphhm3qb5psyfrv850ss4cmqr4i7aw1kc0fvs1j"; depends=[BSgenome]; };
   BSgenome_Vvinifera_URGI_IGGP8X = derive2 { name="BSgenome.Vvinifera.URGI.IGGP8X"; version="0.1"; sha256="0v0hi2pbbi5ynd92bvbv4bzr7bgv48kvyz62hdv7k9gh7s5pg0id"; depends=[BSgenome]; };
-  CTCF = derive2 { name="CTCF"; version="0.99.10"; sha256="0s6rscf6c4sjf6azf3blzb3lfgk7sk3clrlvmhq2gv82g9ic6d40"; depends=[]; };
+  CTCF = derive2 { name="CTCF"; version="0.99.11"; sha256="06gy1f71p01h6yfj5xmvlgz6n7sg7rpkc3723y51h30ir6xrzbrg"; depends=[]; };
   ChemmineDrugs = derive2 { name="ChemmineDrugs"; version="1.0.2"; sha256="0l47ac6lkycmghra2cbcdcxcv47ari8xg6lxpzilvkf4n6ld6064"; depends=[BiocGenerics ChemmineR RSQLite]; };
   DO_db = derive2 { name="DO.db"; version="2.9"; sha256="10bqqa124l61ivzy4mdd3z3ar9a6537qbxw23pc4y9w8a6dwnavn"; depends=[AnnotationDbi]; };
   ENCODExplorerData = derive2 { name="ENCODExplorerData"; version="0.99.5"; sha256="00gfm5l8pxrfs4cw4jlw6n0cz5s31isg69k833n89800v26w3kvh"; depends=[data_table jsonlite RCurl]; };
@@ -219,8 +220,8 @@ in with self; {
   SNPlocs_Hsapiens_dbSNP144_GRCh38 = derive2 { name="SNPlocs.Hsapiens.dbSNP144.GRCh38"; version="0.99.20"; sha256="0yxmsnxncr7w30r0d7bg5i96pclm2vf40p9jdqa02rc67a6sximn"; depends=[BiocGenerics BSgenome GenomeInfoDb GenomicRanges IRanges S4Vectors]; };
   SNPlocs_Hsapiens_dbSNP149_GRCh38 = derive2 { name="SNPlocs.Hsapiens.dbSNP149.GRCh38"; version="0.99.20"; sha256="17bv25p1261hn9d7mxfp6pvivj15pxyvr92gms8a8msfqg9y0xkb"; depends=[BiocGenerics BSgenome GenomeInfoDb GenomicRanges IRanges S4Vectors]; };
   SNPlocs_Hsapiens_dbSNP150_GRCh38 = derive2 { name="SNPlocs.Hsapiens.dbSNP150.GRCh38"; version="0.99.20"; sha256="0jkwwgxxpm9ry8kizq8hs70sky41pks1ag40y5aqq91yjbpqlckj"; depends=[BiocGenerics BSgenome GenomeInfoDb GenomicRanges IRanges S4Vectors]; };
-  SNPlocs_Hsapiens_dbSNP155_GRCh37 = derive2 { name="SNPlocs.Hsapiens.dbSNP155.GRCh37"; version="0.99.22"; sha256="0icb85y6jc6a2rphf8dsxhfcsh7j6kmm6iii7f0dl33dsgsmb1wl"; depends=[BiocGenerics BSgenome GenomeInfoDb GenomicRanges IRanges S4Vectors]; };
-  SNPlocs_Hsapiens_dbSNP155_GRCh38 = derive2 { name="SNPlocs.Hsapiens.dbSNP155.GRCh38"; version="0.99.22"; sha256="1zdx6bjl494wlzqhhz6q6cnygbrvqimcrmmxab5dfwckkyfxlyd8"; depends=[BiocGenerics BSgenome GenomeInfoDb GenomicRanges IRanges S4Vectors]; };
+  SNPlocs_Hsapiens_dbSNP155_GRCh37 = derive2 { name="SNPlocs.Hsapiens.dbSNP155.GRCh37"; version="0.99.23"; sha256="1hl63ph2j8s2igwgp0xs35a366wa7f1x6bmid09k6wqx8fcdilgy"; depends=[BiocGenerics BSgenome GenomeInfoDb GenomicRanges IRanges S4Vectors]; };
+  SNPlocs_Hsapiens_dbSNP155_GRCh38 = derive2 { name="SNPlocs.Hsapiens.dbSNP155.GRCh38"; version="0.99.23"; sha256="0j4skfz6g7ir1igqbql0hk04871vpfqg7dpmvv9z6k2mx9lnrh7w"; depends=[BiocGenerics BSgenome GenomeInfoDb GenomicRanges IRanges S4Vectors]; };
   TxDb_Athaliana_BioMart_plantsmart22 = derive2 { name="TxDb.Athaliana.BioMart.plantsmart22"; version="3.0.1"; sha256="0j2zr4cddad7z1lxx9m9kfgyy7jajjnblpk9j8igd39ia3ixrpzc"; depends=[AnnotationDbi GenomicFeatures]; };
   TxDb_Athaliana_BioMart_plantsmart25 = derive2 { name="TxDb.Athaliana.BioMart.plantsmart25"; version="3.1.3"; sha256="0a6v0l6p13zmiysi3k8dxzdlxng552qqj9rnlbdavdiidla0pvm3"; depends=[AnnotationDbi GenomicFeatures]; };
   TxDb_Athaliana_BioMart_plantsmart28 = derive2 { name="TxDb.Athaliana.BioMart.plantsmart28"; version="3.2.2"; sha256="1yjyvrbx55y024lqg3b2rlf8pngqw5xi3p83j5ipan05wf0aq6ir"; depends=[AnnotationDbi GenomicFeatures]; };
diff --git a/pkgs/development/r-modules/bioc-experiment-packages.nix b/pkgs/development/r-modules/bioc-experiment-packages.nix
index 1888fb3ecfb8..e3666e799cc5 100644
--- a/pkgs/development/r-modules/bioc-experiment-packages.nix
+++ b/pkgs/development/r-modules/bioc-experiment-packages.nix
@@ -22,7 +22,7 @@ in with self; {
   BeadArrayUseCases = derive2 { name="BeadArrayUseCases"; version="1.36.0"; sha256="079qj26622s9jb2kw1wpd5bjihmj3a9mif4y86zjna7jm1jdvzv8"; depends=[beadarray GEOquery limma]; };
   BeadSorted_Saliva_EPIC = derive2 { name="BeadSorted.Saliva.EPIC"; version="1.6.0"; sha256="0mh10sg95djkzp9w7bjr4ggy86a0pakfi2008fk4xikjc3q7ky24"; depends=[ExperimentHub minfi]; };
   BioImageDbs = derive2 { name="BioImageDbs"; version="1.6.0"; sha256="0r4m5qchzglpx4dn95ss0xfd3cqd7vxafjg869y8fxpayjn11dqg"; depends=[animation AnnotationHub EBImage einsum ExperimentHub filesstrings magick magrittr markdown rmarkdown]; };
-  BioPlex = derive2 { name="BioPlex"; version="1.4.2"; sha256="091d9gywkkbgd922sgqqqnj20sjnrsarqrhqbw99x9ccnfzqr2jn"; depends=[BiocFileCache GenomeInfoDb GenomicRanges GEOquery graph SummarizedExperiment]; };
+  BioPlex = derive2 { name="BioPlex"; version="1.4.3"; sha256="01kal3fg1ii6cx33ccar3aaq36a11irg1ac8fcanm5xr4lhsf8v8"; depends=[BiocFileCache GenomeInfoDb GenomicRanges GEOquery graph SummarizedExperiment]; };
   BloodCancerMultiOmics2017 = derive2 { name="BloodCancerMultiOmics2017"; version="1.18.0"; sha256="1284qhij9663b382aq4nq3zl3jjsj5gdh3bfqj6sjfvbvx4pmcpg"; depends=[beeswarm Biobase DESeq2 devtools dplyr ggdendro ggplot2 glmnet gtable ipflasso RColorBrewer reshape2 scales SummarizedExperiment survival tibble]; };
   CCl4 = derive2 { name="CCl4"; version="1.36.0"; sha256="09zja5jzz7lh11cyjvczfgic8z4bq35j6f63irwwizxvp861w902"; depends=[Biobase limma]; };
   CLL = derive2 { name="CLL"; version="1.38.0"; sha256="109sspddzqg08gqf5xacf2vbjs672i2d3n6a6wzr8isdyar40xx1"; depends=[affy Biobase]; };
@@ -131,7 +131,7 @@ in with self; {
   MethylSeqData = derive2 { name="MethylSeqData"; version="1.8.0"; sha256="0rfl5xz23kbvjxf2sf25j526a8252dvd6zmg4x9pj7fqyf7yvfdd"; depends=[ExperimentHub GenomeInfoDb GenomicRanges HDF5Array IRanges rhdf5 S4Vectors SummarizedExperiment]; };
   MicrobiomeBenchmarkData = derive2 { name="MicrobiomeBenchmarkData"; version="1.0.0"; sha256="06m0yi3379g8kvhs0amcc9r5d0np9xwq2a85vk8iz3xi6sqbbbzj"; depends=[ape BiocFileCache S4Vectors SummarizedExperiment TreeSummarizedExperiment]; };
   MouseGastrulationData = derive2 { name="MouseGastrulationData"; version="1.12.0"; sha256="0icgs53mfaiary8gjifasjalc9942fr876w61bxssdg7v4jn76ss"; depends=[BiocGenerics BumpyMatrix ExperimentHub S4Vectors SingleCellExperiment SpatialExperiment SummarizedExperiment]; };
-  MouseThymusAgeing = derive2 { name="MouseThymusAgeing"; version="1.6.0"; sha256="0y5xibhd5w37ks3fvn6gsgqd5whxvg1rbd4li2ank0v56mvazfij"; depends=[BiocGenerics ExperimentHub S4Vectors SingleCellExperiment SummarizedExperiment]; };
+  MouseThymusAgeing = derive2 { name="MouseThymusAgeing"; version="1.6.1"; sha256="11hs19zcpa8bfmidm7v9hll735c6waq37s879mwz4wgxw9ysk1nl"; depends=[BiocGenerics ExperimentHub S4Vectors SingleCellExperiment SummarizedExperiment]; };
   NCIgraphData = derive2 { name="NCIgraphData"; version="1.34.0"; sha256="0sismlawhq1dz29v1532x5ha1n2pdv2fa43kzma4xdf1vafj5ham"; depends=[]; };
   NGScopyData = derive2 { name="NGScopyData"; version="1.18.0"; sha256="1w3hpmqf6030smwb4r61czwz0qsr2kz8z11q8z8819bj0czvr32x"; depends=[]; };
   NanoporeRNASeq = derive2 { name="NanoporeRNASeq"; version="1.8.0"; sha256="0k548ib7yi29xcs2c0y46c3vwi6fkqsp3njwbn4acm85pr93z54g"; depends=[ExperimentHub]; };
@@ -222,7 +222,7 @@ in with self; {
   VectraPolarisData = derive2 { name="VectraPolarisData"; version="1.2.0"; sha256="0gl92bypw6axdwj83dxmvib7p72dl1n5vqfrsy398fahx24djwln"; depends=[ExperimentHub SpatialExperiment]; };
   WES_1KG_WUGSC = derive2 { name="WES.1KG.WUGSC"; version="1.30.0"; sha256="0yi72kdihvrxf7w72fn24bs5r89pg10kc9myl8n4nmf2iiplcn0c"; depends=[]; };
   WGSmapp = derive2 { name="WGSmapp"; version="1.10.0"; sha256="0lgfmpmnwpmrg05nz8vxlkz3jwy6gkd74fl7a2f81bh2lrs4bgh1"; depends=[GenomicRanges]; };
-  WeberDivechaLCdata = derive2 { name="WeberDivechaLCdata"; version="1.0.0"; sha256="1zqc26n7945b024ln82yqp5zpsmb7d5bi8zgj8hqnm09bna3qiil"; depends=[ExperimentHub SingleCellExperiment SpatialExperiment]; };
+  WeberDivechaLCdata = derive2 { name="WeberDivechaLCdata"; version="1.0.1"; sha256="1swdzlcja42adx4j5h82nskbks8lkhbq07gvb9p09q2lg8rylc7q"; depends=[ExperimentHub SingleCellExperiment SpatialExperiment]; };
   XhybCasneuf = derive2 { name="XhybCasneuf"; version="1.36.0"; sha256="1r09wr45vjcr7yxxfi5l132bqg380bicdlz699961hbinvyg7pgc"; depends=[affy ath1121501cdf RColorBrewer tinesath1cdf]; };
   adductData = derive2 { name="adductData"; version="1.14.0"; sha256="0yfgjvq7qk5gvdjhrh2lyz77c6jd438ykd2mpfm6643zr2bkxp4g"; depends=[AnnotationHub ExperimentHub]; };
   affycompData = derive2 { name="affycompData"; version="1.36.0"; sha256="0qcjlm2i0z8z6ab7dknwl1pdmxv69hyfpj61lhygn8ks02al12kn"; depends=[affycomp Biobase]; };
@@ -269,10 +269,10 @@ in with self; {
   curatedBladderData = derive2 { name="curatedBladderData"; version="1.34.0"; sha256="1vp9w40v37xgjdsg8m0w7580h2i0xi823f34qik87mj1hr5xawsf"; depends=[affy]; };
   curatedBreastData = derive2 { name="curatedBreastData"; version="2.26.0"; sha256="02iflnwfpcmglj060w5zygqccii91n2s0vp9bkl1ppj6g409pxm3"; depends=[Biobase BiocStyle ggplot2 impute XML]; };
   curatedCRCData = derive2 { name="curatedCRCData"; version="2.30.0"; sha256="0hbc3d1sj1mfqszmfgkmhpnkbw4mdapp85s7bj2spmcwf0pcsr0n"; depends=[BiocGenerics nlme]; };
-  curatedMetagenomicData = derive2 { name="curatedMetagenomicData"; version="3.6.0"; sha256="0ry9063nmcc5n289a2h7rpv7dgf25i3yk44nfsslfy73bvrdnz75"; depends=[AnnotationHub dplyr ExperimentHub magrittr mia purrr rlang S4Vectors stringr SummarizedExperiment tibble tidyr tidyselect TreeSummarizedExperiment]; };
+  curatedMetagenomicData = derive2 { name="curatedMetagenomicData"; version="3.6.2"; sha256="1qlsjif43pjsm7gkxlvixgpd457q9jgj3ikmvxan4wi6hfw4rxwi"; depends=[AnnotationHub dplyr ExperimentHub magrittr mia purrr rlang S4Vectors stringr SummarizedExperiment tibble tidyr tidyselect TreeSummarizedExperiment]; };
   curatedOvarianData = derive2 { name="curatedOvarianData"; version="1.36.0"; sha256="09zb3m32a2rqwgs2x6g1ixvwnbx0100mb2m8rkbkdlfczlnq9riq"; depends=[affy BiocGenerics]; };
   curatedTBData = derive2 { name="curatedTBData"; version="1.4.0"; sha256="0ksb30h6hlksxzgp0dl1f09jr4a59zdll9jnla8xcsbqqvbkm4g7"; depends=[AnnotationHub ExperimentHub MultiAssayExperiment rlang]; };
-  curatedTCGAData = derive2 { name="curatedTCGAData"; version="1.20.0"; sha256="01q3bcspvff2syg5d933iqfxwl62axfy4xbzkwlg15as7bl7a54r"; depends=[AnnotationHub ExperimentHub HDF5Array MultiAssayExperiment S4Vectors SummarizedExperiment]; };
+  curatedTCGAData = derive2 { name="curatedTCGAData"; version="1.20.1"; sha256="0w3iv044gynhb90bis58dz6znh2fgy7zdgs1yyjzx4fphxzg32j6"; depends=[AnnotationHub ExperimentHub HDF5Array MultiAssayExperiment S4Vectors SummarizedExperiment]; };
   davidTiling = derive2 { name="davidTiling"; version="1.38.0"; sha256="1g8q0m03ss7nf2v3rk6db93mmbzy1kc960scs37pc3s9xdm7k9ak"; depends=[Biobase GO_db tilingArray]; };
   depmap = derive2 { name="depmap"; version="1.12.0"; sha256="10y1s5v6c74ynq8m0rck41w16hglnr700c322k5p9yzndf86f3hv"; depends=[AnnotationHub dplyr ExperimentHub]; };
   derfinderData = derive2 { name="derfinderData"; version="2.16.0"; sha256="147bf7x90prw1x58gy6w13l02sf6zbn4888ikw817k9n5ja3f3x1"; depends=[]; };
diff --git a/pkgs/development/r-modules/bioc-packages.nix b/pkgs/development/r-modules/bioc-packages.nix
index 8e9a7c8b5179..535629b8be23 100644
--- a/pkgs/development/r-modules/bioc-packages.nix
+++ b/pkgs/development/r-modules/bioc-packages.nix
@@ -19,7 +19,7 @@ in with self; {
   ALDEx2 = derive2 { name="ALDEx2"; version="1.30.0"; sha256="0585s5pb8zr9il1vhxw9vjzzajmdcjmf9zz3zlc5vpczd3fnzfkf"; depends=[BiocParallel GenomicRanges IRanges multtest Rfast S4Vectors SummarizedExperiment zCompositions]; };
   AMARETTO = derive2 { name="AMARETTO"; version="1.13.0"; sha256="18w65sf3h4yzw9v5xgkalxnkmgzgsx100v7qc7z4ifx10lgpji5n"; depends=[BiocFileCache callr circlize ComplexHeatmap curatedTCGAData doParallel dplyr DT foreach ggplot2 glmnet gridExtra httr impute knitr limma Matrix matrixStats MultiAssayExperiment Rcpp readr reshape2 rmarkdown tibble]; };
   AMOUNTAIN = derive2 { name="AMOUNTAIN"; version="1.24.0"; sha256="0zzl5dv64yhdivsm2pgsfjikygib9pkfiv34h1lnmqrj6yivvvw8"; depends=[]; };
-  ANCOMBC = derive2 { name="ANCOMBC"; version="2.0.1"; sha256="1bwzvi6j3s66dcll1lb4xy25j4nfn1ln6mc3flh0wgy13l26x8m6"; depends=[CVXR DescTools doParallel doRNG dplyr emmeans energy foreach Hmisc lme4 lmerTest magrittr MASS mia nloptr Rdpack rlang rngtools S4Vectors SingleCellExperiment SummarizedExperiment tibble tidyr TreeSummarizedExperiment]; };
+  ANCOMBC = derive2 { name="ANCOMBC"; version="2.0.2"; sha256="0dlinv4vhxgni8ygzvfw8pbc6d1v9x5chhrpxblhs2c65bkgyxz5"; depends=[CVXR DescTools doParallel doRNG dplyr emmeans energy foreach Hmisc lme4 lmerTest magrittr MASS mia nloptr Rdpack rlang rngtools S4Vectors SingleCellExperiment SummarizedExperiment tibble tidyr TreeSummarizedExperiment]; };
   ANF = derive2 { name="ANF"; version="1.20.0"; sha256="0yfwvgx7144r894fr13sx4gyyq6ljh7y734wx74sb7q80cl2gs1j"; depends=[Biobase igraph MASS RColorBrewer survival]; };
   APAlyzer = derive2 { name="APAlyzer"; version="1.12.0"; sha256="1iaz9ircfh5x3z5pibn5vnd4lbbr7m5ypk97xnizn22z41aqrxn3"; depends=[DESeq2 dplyr GenomicAlignments GenomicFeatures GenomicRanges ggplot2 ggrepel HybridMTest repmis Rsamtools Rsubread rtracklayer SummarizedExperiment tidyr VariantAnnotation]; };
   APL = derive2 { name="APL"; version="1.2.0"; sha256="1i02m70aa67m1h81q9lz3qmc52sc6cjicgxd9krqm9r6fpgcf22g"; depends=[ggplot2 ggrepel magrittr org_Hs_eg_db org_Mm_eg_db plotly reticulate rlang Seurat SingleCellExperiment SummarizedExperiment topGO viridisLite]; };
@@ -44,15 +44,15 @@ in with self; {
   AgiMicroRna = derive2 { name="AgiMicroRna"; version="2.48.0"; sha256="0q3hynyd4dhhh1a2b27y3rrshgvxfwv17k7yabh6g4pc12c33mf7"; depends=[affy affycoretools Biobase limma preprocessCore]; };
   AllelicImbalance = derive2 { name="AllelicImbalance"; version="1.36.0"; sha256="0zn8pp4pl5wr957mf6agjpn61f9qpnjx0nbxb5wnbr40672x0263"; depends=[AnnotationDbi BiocGenerics Biostrings BSgenome GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges gridExtra Gviz IRanges lattice latticeExtra nlme Rsamtools S4Vectors seqinr SummarizedExperiment VariantAnnotation]; };
   AlphaBeta = derive2 { name="AlphaBeta"; version="1.12.0"; sha256="000apg879li9wkbyrl8cm73z6h0xasqp41h9ir9hywy2v38rmc5b"; depends=[BiocParallel data_table dplyr expm ggplot2 gtools igraph optimx plotly stringr]; };
-  AlpsNMR = derive2 { name="AlpsNMR"; version="4.0.2"; sha256="1y4qqc6l8flv5ns4qwzjwmcykm6zcm4jg097mn8xyp7mnxymy7pl"; depends=[baseline BiocParallel dplyr fs future generics ggplot2 glue htmltools magrittr matrixStats mixOmics pcaPP purrr readxl reshape2 rlang rmarkdown scales signal speaq stringr tibble tidyr tidyselect vctrs]; };
+  AlpsNMR = derive2 { name="AlpsNMR"; version="4.0.4"; sha256="19j97qsa1vnxw05dlllbwzdap0xgnmgxyqbi5dy8w2ppwdzxgsfv"; depends=[baseline BiocParallel cli dplyr fs future generics ggplot2 glue htmltools magrittr matrixStats mixOmics pcaPP purrr readxl reshape2 rlang rmarkdown scales signal speaq stringr tibble tidyr tidyselect vctrs]; };
   AnVIL = derive2 { name="AnVIL"; version="1.10.1"; sha256="0iqsffkrxv28g9cddx2w05f2dbscwxhh6bpizwa8xaxhvn5bcpsv"; depends=[BiocManager dplyr DT futile_logger htmltools httr jsonlite miniUI rapiclient rlang shiny tibble tidyr tidyselect]; };
   AnVILBilling = derive2 { name="AnVILBilling"; version="1.8.0"; sha256="13qcp2s012ai44dkddk71ga44y87jnl0vljyd93lj1dlh8nw7c00"; depends=[bigrquery DBI dplyr DT ggplot2 lubridate magrittr plotly shiny shinytoastr]; };
   AnVILPublish = derive2 { name="AnVILPublish"; version="1.8.0"; sha256="1i5zf7pyrzi6v13gpscmdb5qdb5gknicc8fk9s9nmsl1wpj6wlsw"; depends=[AnVIL httr jsonlite readr rmarkdown whisker yaml]; };
   Anaquin = derive2 { name="Anaquin"; version="2.22.0"; sha256="08y2syaacy15rxcf3x2r3906kfm58fkx7ainaqvy5inlc9f670j5"; depends=[DESeq2 ggplot2 knitr locfit plyr qvalue ROCR]; };
   AneuFinder = derive2 { name="AneuFinder"; version="1.26.0"; sha256="154cg63n7h9h5jkj00aqf0hzbmmjg16bzvvk50fyixwq0a4q1j00"; depends=[AneuFinderData bamsignals BiocGenerics Biostrings cowplot DNAcopy doParallel ecp foreach GenomeInfoDb GenomicAlignments GenomicRanges ggdendro ggplot2 ggrepel IRanges mclust reshape2 Rsamtools S4Vectors]; };
-  AnnotationDbi = derive2 { name="AnnotationDbi"; version="1.60.0"; sha256="1srv0jizmwgmsmgb9cfgy5nbgd3jsgxgzzax6wfsahckb5zihrqp"; depends=[Biobase BiocGenerics DBI IRanges KEGGREST RSQLite S4Vectors]; };
+  AnnotationDbi = derive2 { name="AnnotationDbi"; version="1.60.2"; sha256="1c7f2vgdnh99zp83pvmghb7l0rihdijlhdj6ff992h7wrrha8lhg"; depends=[Biobase BiocGenerics DBI IRanges KEGGREST RSQLite S4Vectors]; };
   AnnotationFilter = derive2 { name="AnnotationFilter"; version="1.22.0"; sha256="0m16kfssxbblf03ykawkmqa038cl90prhb23k6y88g2hwm00wynk"; depends=[GenomicRanges lazyeval]; };
-  AnnotationForge = derive2 { name="AnnotationForge"; version="1.40.0"; sha256="15shh8rmcx69g3zd256720vh0c3qbly5zrvwm463dws41cjla48x"; depends=[AnnotationDbi Biobase BiocGenerics DBI RCurl RSQLite S4Vectors XML]; };
+  AnnotationForge = derive2 { name="AnnotationForge"; version="1.40.1"; sha256="16wdcl56d5i8wrmin610kzs9ldy7h9w5fbnysjb1crkcgbikq1yy"; depends=[AnnotationDbi Biobase BiocGenerics DBI RCurl RSQLite S4Vectors XML]; };
   AnnotationHub = derive2 { name="AnnotationHub"; version="3.6.0"; sha256="1hk02q6mwx49khbhydndfa1qry8ylhmwz2dff8845a510hm0di7n"; depends=[AnnotationDbi BiocFileCache BiocGenerics BiocManager BiocVersion curl dplyr httr interactiveDisplayBase rappdirs RSQLite S4Vectors yaml]; };
   AnnotationHubData = derive2 { name="AnnotationHubData"; version="1.28.0"; sha256="0mcx09kcxccw2gkf4c3w7sxgb7v3gwbvahvx9wgq8f93q85yzg95"; depends=[AnnotationDbi AnnotationForge AnnotationHub Biobase BiocCheck BiocGenerics BiocManager biocViews Biostrings DBI futile_logger GenomeInfoDb GenomicFeatures GenomicRanges graph IRanges jsonlite OrganismDbi RCurl Rsamtools RSQLite rtracklayer S4Vectors XML]; };
   ArrayExpress = derive2 { name="ArrayExpress"; version="1.57.0"; sha256="1fzi951mjc4kbkkvlfvwlfrpfnjckkmw4xz4m5dapy1z2jkgp8w6"; depends=[Biobase limma oligo XML]; };
@@ -61,12 +61,12 @@ in with self; {
   BAC = derive2 { name="BAC"; version="1.58.0"; sha256="00dkhns9n1x4wmlxjcw75h7iwwk37zlv1c2fi0g1mmsw1xvdjzp6"; depends=[]; };
   BADER = derive2 { name="BADER"; version="1.36.0"; sha256="1hkvmfik4m2yw5xg4k2g551l27i64blbsdvp1kmvvyix66p53hsr"; depends=[]; };
   BAGS = derive2 { name="BAGS"; version="2.38.0"; sha256="0rnaahbdqpgl666w9xlm6prrrnks2k6p83r625j1lcj2v533232r"; depends=[Biobase breastCancerVDX]; };
-  BANDITS = derive2 { name="BANDITS"; version="1.14.0"; sha256="18xq8gg1j07gbbxy7r0cc34zwn40mh4fr39zzi8l3z0cymw73qs8"; depends=[BiocParallel data_table doParallel doRNG DRIMSeq foreach ggplot2 MASS R_utils Rcpp RcppArmadillo]; };
-  BASiCS = derive2 { name="BASiCS"; version="2.10.2"; sha256="06mp74kchxj2gq0n4rgxfvsm2p92hwd0zy05zq5fnig8mkqkq8sq"; depends=[assertthat Biobase BiocGenerics BiocParallel coda cowplot ggExtra ggplot2 hexbin MASS Matrix matrixStats Rcpp RcppArmadillo reshape2 S4Vectors scran scuttle SingleCellExperiment SummarizedExperiment viridis]; };
+  BANDITS = derive2 { name="BANDITS"; version="1.14.2"; sha256="11w0azh2g0y331imqpllnb0csjxf3gs1767cc67c1zp0ykg6yq8l"; depends=[BiocParallel data_table doParallel doRNG DRIMSeq foreach ggplot2 MASS R_utils Rcpp RcppArmadillo]; };
+  BASiCS = derive2 { name="BASiCS"; version="2.10.5"; sha256="0ipbr7103sisw1pdb5pm4s5fa8g6a14s86zg01wgcinl11kb8vkh"; depends=[assertthat Biobase BiocGenerics BiocParallel coda cowplot ggExtra ggplot2 hexbin MASS Matrix matrixStats Rcpp RcppArmadillo reshape2 S4Vectors scran scuttle SingleCellExperiment SummarizedExperiment viridis]; };
   BASiCStan = derive2 { name="BASiCStan"; version="1.0.0"; sha256="1an4kiipb3y1xixynpka0k2pdsi7a4s6h2mw2yfnwab1q6qf97kj"; depends=[BASiCS BH glmGamPoi Rcpp RcppEigen RcppParallel rstan rstantools scran scuttle SingleCellExperiment StanHeaders SummarizedExperiment]; };
   BBCAnalyzer = derive2 { name="BBCAnalyzer"; version="1.28.0"; sha256="01n9msbnr4x6hjlvz9z43lyrbxnmhi6bc655ir4cq0vizm1mk84m"; depends=[Biostrings GenomicRanges IRanges Rsamtools SummarizedExperiment VariantAnnotation]; };
   BCRANK = derive2 { name="BCRANK"; version="1.60.0"; sha256="01ibjaym2kyv4x0fwv8mk5mq550lm1pqgrq40spmyrgb4vnwkh0h"; depends=[Biostrings]; };
-  BDMMAcorrect = derive2 { name="BDMMAcorrect"; version="1.16.0"; sha256="0d73w5pcca6d4dscw12hwy823ls4xhvdyi2xbiixm9n0rx23wls1"; depends=[ape ellipse ggplot2 Rcpp RcppArmadillo RcppEigen SummarizedExperiment vegan]; };
+  BDMMAcorrect = derive2 { name="BDMMAcorrect"; version="1.16.2"; sha256="1g6j9ygvzcm4dx3h27b94ws1hnhn2kj60z4c77q20ry45an9b3zs"; depends=[ape ellipse ggplot2 Rcpp RcppArmadillo RcppEigen SummarizedExperiment vegan]; };
   BEARscc = derive2 { name="BEARscc"; version="1.18.0"; sha256="1j430ijy2b2j5x1y276vya25pw0qrcl2q11smr394jf4b9hm60qr"; depends=[data_table ggplot2 SingleCellExperiment]; };
   BEAT = derive2 { name="BEAT"; version="1.36.0"; sha256="0b48ravaaqbqvw35bamalrjnp77gqf13rp11wpd86m9ghpjl4gr0"; depends=[Biostrings BSgenome GenomicRanges ShortRead]; };
   BEclear = derive2 { name="BEclear"; version="2.14.0"; sha256="05znaj2fialxi937mhj2dlrm3v4j2wgqafcy78qrkz7xxn13pr01"; depends=[abind BiocParallel data_table dixonTest futile_logger ids Matrix Rcpp Rdpack]; };
@@ -74,15 +74,15 @@ in with self; {
   BHC = derive2 { name="BHC"; version="1.50.0"; sha256="0ryd9lg8pywqlxj802y9jad5nxy40ivnzdq2ldldypwyalgk9ahm"; depends=[]; };
   BLMA = derive2 { name="BLMA"; version="1.22.0"; sha256="0jxxf4g0j5prarjq18ab435h963h1d7mlb4ssj2919lf98rhxl0r"; depends=[Biobase graph GSA limma metafor PADOG ROntoTools]; };
   BOBaFIT = derive2 { name="BOBaFIT"; version="1.2.0"; sha256="0shv241jkzcyp1mydxpg6sjf74zxmc8dpsxdniw7c6arjfv4b39z"; depends=[dplyr GenomicRanges ggbio ggforce ggplot2 magrittr NbClust plyranges stringr tidyr]; };
-  BPRMeth = derive2 { name="BPRMeth"; version="1.24.0"; sha256="0w97b34d6i0n4bvq8a63da1bnkmhhd2sclwhsixlacisgy5hdfls"; depends=[assertthat BiocStyle cowplot data_table doParallel e1071 earth foreach GenomicRanges ggplot2 IRanges kernlab magrittr MASS matrixcalc mvtnorm randomForest Rcpp RcppArmadillo S4Vectors truncnorm]; };
+  BPRMeth = derive2 { name="BPRMeth"; version="1.24.2"; sha256="1nmjqcqhnq8zvssglqqlp8k46q3x2zlvzjnrszcpy0caq4c86m88"; depends=[assertthat BiocStyle cowplot data_table doParallel e1071 earth foreach GenomicRanges ggplot2 IRanges kernlab magrittr MASS matrixcalc mvtnorm randomForest Rcpp RcppArmadillo S4Vectors truncnorm]; };
   BRAIN = derive2 { name="BRAIN"; version="1.44.0"; sha256="1rp2aa7jigi8h3qa55a1pf5zj06a5fpyqxwpc92w8gb0flmmdbn8"; depends=[Biostrings lattice PolynomF]; };
   BRGenomics = derive2 { name="BRGenomics"; version="1.10.0"; sha256="1mdf8v2768vm1wfrcia9cs0biv51hybwa6nraddhccx25cnz1prj"; depends=[DESeq2 GenomeInfoDb GenomicAlignments GenomicRanges IRanges Rsamtools rtracklayer S4Vectors SummarizedExperiment]; };
-  BSgenome = derive2 { name="BSgenome"; version="1.66.1"; sha256="1gzpvajw5n3qmym3312qaks450sq3w456kj4gqwaabgpjxbq7frm"; depends=[BiocGenerics Biostrings GenomeInfoDb GenomicRanges IRanges matrixStats Rsamtools rtracklayer S4Vectors XVector]; };
+  BSgenome = derive2 { name="BSgenome"; version="1.66.3"; sha256="1ps7s6i9mv8ys8k2xw8fdkh2rl2n3kcf2q4zsz6kcz5qpav95ys6"; depends=[BiocGenerics Biostrings GenomeInfoDb GenomicRanges IRanges matrixStats Rsamtools rtracklayer S4Vectors XVector]; };
   BUMHMM = derive2 { name="BUMHMM"; version="1.22.0"; sha256="1llxj25bjq68963nvr4b1n84400w6qb2gaa8jv7if4w8kslv5wvf"; depends=[Biostrings devtools gtools IRanges stringi SummarizedExperiment]; };
   BUS = derive2 { name="BUS"; version="1.54.0"; sha256="1bv50vx4dyb1cz502nqknyss5vfh9cwnms65gcyrii5xydjxr1ch"; depends=[infotheo minet]; };
   BUScorrect = derive2 { name="BUScorrect"; version="1.16.0"; sha256="05a8sn7rd4d3qx46gr742aqgf0968ni2s238z0gxbg8sifjphii7"; depends=[gplots SummarizedExperiment]; };
-  BUSpaRse = derive2 { name="BUSpaRse"; version="1.12.0"; sha256="1hnlgqd6igcpq6kfmj82v1m07ndq3nsx4iiv3j37gxy5pi367026"; depends=[AnnotationDbi AnnotationFilter BH BiocGenerics biomaRt Biostrings BSgenome dplyr ensembldb GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 IRanges magrittr Matrix plyranges Rcpp RcppArmadillo RcppProgress S4Vectors stringr tibble tidyr zeallot]; };
-  BUSseq = derive2 { name="BUSseq"; version="1.4.0"; sha256="0ydryxgas192fsyvivwjjrghz9jgxnvaq3igchmwvl50yxnggmzb"; depends=[gplots S4Vectors SingleCellExperiment SummarizedExperiment]; };
+  BUSpaRse = derive2 { name="BUSpaRse"; version="1.12.2"; sha256="15w2363bgllw1p6h7327qx28kip0cq7s0x7da7r56yfkm0xag4rg"; depends=[AnnotationDbi AnnotationFilter BH BiocGenerics biomaRt Biostrings BSgenome dplyr ensembldb GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 IRanges magrittr Matrix plyranges Rcpp RcppArmadillo RcppProgress S4Vectors stringr tibble tidyr zeallot]; };
+  BUSseq = derive2 { name="BUSseq"; version="1.4.2"; sha256="0s0kkfn45nfwv92962spf7v4kax24ldnwxipkqsfk0is57312syn"; depends=[gplots S4Vectors SingleCellExperiment SummarizedExperiment]; };
   BaalChIP = derive2 { name="BaalChIP"; version="1.24.0"; sha256="16s67v6mkv14dkk1r7c50brm7198b84h87h1wrahmrrcnzq8pi0n"; depends=[coda doBy doParallel foreach GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 IRanges reshape2 Rsamtools scales]; };
   BadRegionFinder = derive2 { name="BadRegionFinder"; version="1.26.0"; sha256="0bsgdjchwsfc8aiwiacr454kw97dbymq6v450m1fx7hxmmpqz1sm"; depends=[biomaRt GenomicRanges Rsamtools S4Vectors VariantAnnotation]; };
   BaseSpaceR = derive2 { name="BaseSpaceR"; version="1.42.0"; sha256="07pqs0jkwcbxavc65sanvhvzc9spkk46bqnwz162f3pvrz15b5h7"; depends=[RCurl RJSONIO]; };
@@ -90,7 +90,7 @@ in with self; {
   BasicSTARRseq = derive2 { name="BasicSTARRseq"; version="1.26.0"; sha256="1yk4zpgwy5dcgimqp9w7hscvg2irgr281f8zv8rp576c8xbzqgqz"; depends=[GenomeInfoDb GenomicAlignments GenomicRanges IRanges S4Vectors]; };
   BatchQC = derive2 { name="BatchQC"; version="1.26.0"; sha256="1rjqldr9vp8ppcwbclm8cvkpsncss31n449s6nsczmv517mjna1q"; depends=[corpcor ggvis gplots heatmaply knitr limma Matrix matrixStats MCMCpack moments pander reshape2 rmarkdown shiny sva]; };
   BayesKnockdown = derive2 { name="BayesKnockdown"; version="1.24.0"; sha256="1r4d3h6fvn946czpf81prqwycvkgmzlcypy8dl54diagvdp3dr9y"; depends=[Biobase]; };
-  BayesSpace = derive2 { name="BayesSpace"; version="1.8.0"; sha256="1hqlr82fribkw9vs7fjwqr0impz7f5wfdm7q19ny17k8ald6mh21"; depends=[assertthat BiocFileCache BiocSingular coda DirichletReg ggplot2 Matrix mclust purrr Rcpp RcppArmadillo RcppDist RcppProgress RCurl rhdf5 S4Vectors scales scater scran SingleCellExperiment SummarizedExperiment xgboost]; };
+  BayesSpace = derive2 { name="BayesSpace"; version="1.8.2"; sha256="0a9idbj8n3n6rw38jiicpgh69jqah9p58ag9qf8qljb4fz51y4v1"; depends=[assertthat BiocFileCache BiocSingular coda DirichletReg ggplot2 Matrix mclust purrr Rcpp RcppArmadillo RcppDist RcppProgress RCurl rhdf5 S4Vectors scales scater scran SingleCellExperiment SummarizedExperiment xgboost]; };
   BeadDataPackR = derive2 { name="BeadDataPackR"; version="1.50.0"; sha256="0309cvc9aq4nb06zysb7jvzd844pvw6jbjiqwhar6fg01cx255j0"; depends=[]; };
   BgeeCall = derive2 { name="BgeeCall"; version="1.14.0"; sha256="05w6b10vc4mmwdqnkcj7vnfigk03f03n776vqhlb38k0lx8k4hk3"; depends=[biomaRt Biostrings data_table dplyr GenomicFeatures jsonlite rhdf5 rslurm rtracklayer sjmisc tximport]; };
   BgeeDB = derive2 { name="BgeeDB"; version="2.24.0"; sha256="14fja1dikzq60zjx1arcv1q16qd0hmibqjy0nbaivmk3zh16spkc"; depends=[Biobase curl data_table digest dplyr graph R_utils RCurl RSQLite tidyr topGO]; };
@@ -111,19 +111,19 @@ in with self; {
   BioTIP = derive2 { name="BioTIP"; version="1.12.0"; sha256="1n90n4vz0cwz8irwpmrkm9qcyvk5rssl2v6wrzny4zwhzjkmvlni"; depends=[cluster GenomicRanges igraph MASS psych scran stringr]; };
   Biobase = derive2 { name="Biobase"; version="2.58.0"; sha256="0rp541nphbcya6kbk1nzrrb05g5m6pxb3yqz5cj873di9vsqlyfv"; depends=[BiocGenerics]; };
   BiocBaseUtils = derive2 { name="BiocBaseUtils"; version="1.0.0"; sha256="0p6siidrx8q6qr36fc67hzi091m2zwik3zngj27yllbfz6sn5k69"; depends=[]; };
-  BiocCheck = derive2 { name="BiocCheck"; version="1.34.2"; sha256="1zj43kbzvi2ws8c182fp6vn5r6iiqsr6p2iyy3k8n3ifm2acqw2h"; depends=[BiocManager biocViews codetools graph httr knitr stringdist]; };
+  BiocCheck = derive2 { name="BiocCheck"; version="1.34.3"; sha256="00z2l5jnc028bmd3rl3qmgkd6k1mfa4p68kls34mkn29ic9ls22m"; depends=[BiocManager biocViews codetools graph httr knitr stringdist]; };
   BiocDockerManager = derive2 { name="BiocDockerManager"; version="1.10.0"; sha256="13l5shmiiv4wl9m5xnwzagjxqrchjg9znvcgf7hv8f263l2yc8qm"; depends=[dplyr httr memoise readr whisker]; };
   BiocFHIR = derive2 { name="BiocFHIR"; version="1.0.0"; sha256="1b0mychyv778cf2jmib15jpjmh83s4sjr69qrjgmv0c7kvv4msf7"; depends=[BiocBaseUtils DT graph igraph jsonlite shiny tidyr visNetwork]; };
-  BiocFileCache = derive2 { name="BiocFileCache"; version="2.6.0"; sha256="0skrvmkm6ch8gbpdi4wr59zk5vxzxs7cyqvz3jhki9d8w492wylg"; depends=[curl DBI dbplyr dplyr filelock httr rappdirs RSQLite]; };
+  BiocFileCache = derive2 { name="BiocFileCache"; version="2.6.1"; sha256="16316a5pgyl5rppyviibf6z3k3m7xmvqyylf1kxdpg0avs6dk8w7"; depends=[curl DBI dbplyr dplyr filelock httr rappdirs RSQLite]; };
   BiocGenerics = derive2 { name="BiocGenerics"; version="0.44.0"; sha256="17dhr7vaph8dnvyklszyas7y8i64mxqxhnfhb6q3l47gq5if8645"; depends=[]; };
   BiocIO = derive2 { name="BiocIO"; version="1.8.0"; sha256="15d4xsn3k32q7lzcyxvs70f0jbh9fgwl3vi7xd6sqpggar12hh9f"; depends=[BiocGenerics S4Vectors]; };
   BiocNeighbors = derive2 { name="BiocNeighbors"; version="1.16.0"; sha256="09f00rf5gwwlxxaycsciq4l53gjg5kjayx8xzhns2yf1fv297j9p"; depends=[BiocParallel Matrix Rcpp RcppHNSW S4Vectors]; };
   BiocOncoTK = derive2 { name="BiocOncoTK"; version="1.18.0"; sha256="1x4mzzjvjgcxg5xyxjib8r2n55hpf2vzcci0xkb7d8frakfncn9s"; depends=[bigrquery car ComplexHeatmap curatedTCGAData DBI dplyr DT GenomicFeatures GenomicRanges ggplot2 ggpubr graph httr IRanges magrittr plyr Rgraphviz rjson S4Vectors scales shiny SummarizedExperiment]; };
-  BiocParallel = derive2 { name="BiocParallel"; version="1.32.4"; sha256="1m4i27zx3ajwygwp38lrxf36rs575dkaxxc6jawpj1kzn7whi5ym"; depends=[BH codetools cpp11 futile_logger snow]; };
-  BiocPkgTools = derive2 { name="BiocPkgTools"; version="1.16.0"; sha256="1av7vnw6z9cw7j4d3vpi8mfs5h4pn4yr2wc8ybg7ad1d686ah845"; depends=[BiocFileCache BiocManager biocViews dplyr DT gh graph htmltools htmlwidgets httr igraph jsonlite magrittr RBGL readr rlang rorcid rvest stringr tibble xml2]; };
-  BiocSet = derive2 { name="BiocSet"; version="1.12.0"; sha256="197cy5gdlvac7jqwb4dm4dbqfms2nvc3paqs75nsg9mpp1h5z8l8"; depends=[AnnotationDbi BiocIO dplyr KEGGREST ontologyIndex plyr rlang S4Vectors tibble tidyr]; };
+  BiocParallel = derive2 { name="BiocParallel"; version="1.32.5"; sha256="1yd6ln9cl3dcvfziar52fkvqi2lzm31l7j21r1rwl1mpkz0xapir"; depends=[BH codetools cpp11 futile_logger snow]; };
+  BiocPkgTools = derive2 { name="BiocPkgTools"; version="1.16.1"; sha256="0cl88adkbxv7sz07b8h5qpwwkwg85jx6xjinkd0yjac4xm7s4lyf"; depends=[BiocFileCache BiocManager biocViews dplyr DT gh graph htmltools htmlwidgets httr igraph jsonlite magrittr RBGL readr rlang rorcid rvest stringr tibble xml2]; };
+  BiocSet = derive2 { name="BiocSet"; version="1.12.1"; sha256="1cqp5m6yic5vsp8k05r50sx2cmi9cwzxfmlswcjw28nascq3gpv0"; depends=[AnnotationDbi BiocIO dplyr KEGGREST ontologyIndex plyr rlang S4Vectors tibble tidyr]; };
   BiocSingular = derive2 { name="BiocSingular"; version="1.14.0"; sha256="041izymcifvi0pa97fh5000bwlyl0mdk9003i5bbvlld6mbbv2kk"; depends=[beachmat BiocGenerics BiocParallel DelayedArray irlba Matrix Rcpp rsvd S4Vectors ScaledMatrix]; };
-  BiocSklearn = derive2 { name="BiocSklearn"; version="1.20.0"; sha256="049j8rq17k84mw4pa9zgcn6814bdq4m5xcrxp730j183h8wly742"; depends=[basilisk basilisk_utils reticulate SummarizedExperiment]; };
+  BiocSklearn = derive2 { name="BiocSklearn"; version="1.20.1"; sha256="17hgqy6n38ga221p5sxhbsahhbs81bmyx1vfg127cx3dpv5lq5vd"; depends=[basilisk reticulate SummarizedExperiment]; };
   BiocStyle = derive2 { name="BiocStyle"; version="2.26.0"; sha256="092hpmyhra755j32vc8w2l6xqwg09jm8apnk5rvxi1cm5034yvsl"; depends=[BiocManager bookdown knitr rmarkdown yaml]; };
   BiocVersion = derive2 { name="BiocVersion"; version="3.16.0"; sha256="1djp23y131dyx4g22f9r7an177bq0mky94bvpqvc8b14166g0ynw"; depends=[]; };
   BiocWorkflowTools = derive2 { name="BiocWorkflowTools"; version="1.24.0"; sha256="00cy5lqmfap57bm2s00bis9ddci2lv1lrp0mk5ydgx061p4ym29i"; depends=[BiocStyle bookdown git2r httr knitr rmarkdown rstudioapi stringr usethis]; };
@@ -148,7 +148,7 @@ in with self; {
   CCPROMISE = derive2 { name="CCPROMISE"; version="1.24.0"; sha256="1iwvmw7k64n41qggxjxk3jbhrhpdnwfgn6vbm3cy467kpfzbzrzg"; depends=[Biobase CCP GSEABase PROMISE]; };
   CEMiTool = derive2 { name="CEMiTool"; version="1.22.0"; sha256="15dm4ajhnf7wv1cs6kfpp4sxfqyl0x11d1bzjagwxk7c911p4a8x"; depends=[clusterProfiler data_table dplyr DT fastcluster fgsea ggdendro ggplot2 ggpmisc ggrepel ggthemes gridExtra gtable htmltools igraph intergraph knitr matrixStats network pracma rmarkdown scales sna stringr WGCNA]; };
   CFAssay = derive2 { name="CFAssay"; version="1.32.0"; sha256="0lm7281d7gvdlkk35195zi2kjs0xj7jnr3gwkjgrvn6qhi0dk2vr"; depends=[]; };
-  CGEN = derive2 { name="CGEN"; version="3.34.1"; sha256="12xnnnllpkgxi7vl8x97ib5mldh2b2kh66klhm1hkk0yfj3nrax8"; depends=[mvtnorm survival]; };
+  CGEN = derive2 { name="CGEN"; version="3.34.3"; sha256="0viymdgfnc16mihi31fd5wpbbr57b3kaz55p9sg2rzrw3br6cqyq"; depends=[mvtnorm survival]; };
   CGHbase = derive2 { name="CGHbase"; version="1.58.0"; sha256="01n1z525h4h6yr3jfalgjg2g6lhd77sc3n33q0485x7l6xqv1dvp"; depends=[Biobase marray]; };
   CGHcall = derive2 { name="CGHcall"; version="2.60.0"; sha256="0860w2vf662qqii09pjdx85yl346jcldxiikhbwv0vg86blwb2g2"; depends=[Biobase CGHbase DNAcopy impute snowfall]; };
   CGHnormaliter = derive2 { name="CGHnormaliter"; version="1.52.0"; sha256="08s3mdsaqv92f6mjj4mg1m7b13zpfm7c144mv754pnpfay2slw88"; depends=[Biobase CGHbase CGHcall]; };
@@ -158,7 +158,7 @@ in with self; {
   CIMICE = derive2 { name="CIMICE"; version="1.6.0"; sha256="0w3rx643ing2i1b71fhcmqm9pbrw7q206lk7ncml3gaaw13lf6hc"; depends=[assertthat dplyr expm ggcorrplot ggplot2 ggraph glue igraph maftools Matrix networkD3 purrr tidygraph tidyr visNetwork]; };
   CINdex = derive2 { name="CINdex"; version="1.26.0"; sha256="186akmq5s81849pa56f3cqdacrmip2h9i0n67qkv9jnxk1l3h2x3"; depends=[bitops dplyr GenomeInfoDb GenomicRanges gplots gridExtra IRanges png S4Vectors som stringr]; };
   CMA = derive2 { name="CMA"; version="1.56.0"; sha256="13qdhg5w1yga5sb4vack2srx5ly126g740wbxb55cg1kyqnzs1pd"; depends=[Biobase]; };
-  CNAnorm = derive2 { name="CNAnorm"; version="1.44.1"; sha256="1f7y609q007mrjjwrs2q26yfgafaydim0van3v6p42x20k0n30y8"; depends=[DNAcopy]; };
+  CNAnorm = derive2 { name="CNAnorm"; version="1.44.3"; sha256="1xzlxqmipyky86gh169njil8jvha0rnz9cgby1grzwlm5kjqqxsa"; depends=[DNAcopy]; };
   CNEr = derive2 { name="CNEr"; version="1.34.0"; sha256="15y27ca14fdhn2prqgkyikff7p7490xn0bp2c7cnwhw173mm1syw"; depends=[annotate BiocGenerics Biostrings DBI GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 GO_db IRanges KEGGREST poweRlaw R_utils readr reshape2 RSQLite rtracklayer S4Vectors XVector]; };
   CNORdt = derive2 { name="CNORdt"; version="1.40.0"; sha256="0ybxps1dnl7v7p68vkxqjr7f7zbmaqnh9x2gq1vzhcgzv767p1jz"; depends=[abind CellNOptR]; };
   CNORfeeder = derive2 { name="CNORfeeder"; version="1.38.0"; sha256="0y8wmm4sb28k4hk9cc59wqk1im79z13ahm232dcqh78772cw5w0h"; depends=[CellNOptR graph]; };
@@ -175,7 +175,7 @@ in with self; {
   COCOA = derive2 { name="COCOA"; version="2.12.0"; sha256="01879lxdzxbg77sd5r8rw59kaa9s5jrsfnd2na68hsv41vhs64xf"; depends=[Biobase BiocGenerics ComplexHeatmap data_table fitdistrplus GenomicRanges ggplot2 IRanges MIRA S4Vectors simpleCache tidyr]; };
   CODEX = derive2 { name="CODEX"; version="1.30.0"; sha256="1wrxzdk0ldkb2svgi84gvmkg97m3fv71937harzhmwhfwbk2mlc6"; depends=[Biostrings BSgenome_Hsapiens_UCSC_hg19 GenomeInfoDb IRanges Rsamtools S4Vectors]; };
   COHCAP = derive2 { name="COHCAP"; version="1.44.0"; sha256="0nmnvnz8qli5xxzdnps0ndyjniixd4qpm8kbigmyqi0zviha588i"; depends=[BH COHCAPanno gplots RColorBrewer Rcpp RcppArmadillo WriteXLS]; };
-  COMPASS = derive2 { name="COMPASS"; version="1.36.0"; sha256="16wc5cipsl37707v1ffqpr55dks0m9ygv5a8v2llgdjd176dz1pd"; depends=[abind BiocStyle clue coda data_table dplyr foreach knitr magrittr pdist plyr RColorBrewer Rcpp reshape2 rlang rmarkdown scales tidyr]; };
+  COMPASS = derive2 { name="COMPASS"; version="1.36.2"; sha256="0bszxfwayqnkpp715r1c2pwwkavwh8dfqlr41k6aqjbn230aniv6"; depends=[abind BiocStyle clue coda data_table dplyr foreach knitr magrittr pdist plyr RColorBrewer Rcpp reshape2 rlang rmarkdown scales tidyr]; };
   CONFESS = derive2 { name="CONFESS"; version="1.26.0"; sha256="10yz0nwssgak0gndw9py5yksdq1syb7dfa33kvkhf5ljwyxf955c"; 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="1.6.0"; sha256="1mkzmjqsm9kqlabw50d8jn0jqx2iad1wn10il4j473bhamanwqg4"; depends=[]; };
   CORREP = derive2 { name="CORREP"; version="1.64.0"; sha256="07pr5v8sqzlvag1yapaz01pl54c8ab1gdq2hinhwv2kiyyxpkq11"; depends=[e1071]; };
@@ -193,7 +193,7 @@ in with self; {
   Cardinal = derive2 { name="Cardinal"; version="3.0.1"; sha256="0n8760dfwc5qna6v4b7sxwr20rk10pj2alp259ypgmpb2ryk01sl"; depends=[Biobase BiocGenerics BiocParallel EBImage irlba magrittr Matrix matter mclust nlme ProtGenerics S4Vectors signal sp viridisLite]; };
   Category = derive2 { name="Category"; version="2.64.0"; sha256="1j62b3ycvb27p80k1a1qj4pdf8cjynf5fkj65v74c3l1hgl9qxnh"; depends=[annotate AnnotationDbi Biobase BiocGenerics DBI genefilter graph GSEABase Matrix RBGL]; };
   CausalR = derive2 { name="CausalR"; version="1.30.0"; sha256="0nxiwnln696v3hw1m19whpajzqfb6y0c9dn3v154l7n84v0j5wd2"; depends=[igraph]; };
-  CeTF = derive2 { name="CeTF"; version="1.9.0"; sha256="07hzw8ynywfyvac3xm7llvs67mnlixjw5y9rz3sfvbfssnz5ihh2"; depends=[circlize clusterProfiler ComplexHeatmap DESeq2 dplyr GenomicTools_fileHandler GGally ggnetwork ggplot2 ggpubr ggrepel igraph Matrix network Rcpp RcppArmadillo RCy3 S4Vectors SummarizedExperiment]; };
+  CeTF = derive2 { name="CeTF"; version="1.10.2"; sha256="12sylkz8spvpbbb3rbibbsnv7g2b795h1n9bfxjf51yykdcknrb3"; depends=[circlize clusterProfiler ComplexHeatmap DESeq2 dplyr GenomicTools_fileHandler GGally ggnetwork ggplot2 ggpubr ggrepel igraph Matrix network Rcpp RcppArmadillo RCy3 S4Vectors SummarizedExperiment]; };
   CellBarcode = derive2 { name="CellBarcode"; version="1.4.0"; sha256="0kiariwn252ri27gsdy7924i98akx8bmpgr76f7s395hrhlrc36d"; depends=[BH Biostrings Ckmeans_1d_dp data_table egg ggplot2 magrittr plyr Rcpp S4Vectors seqinr ShortRead stringr zlibbioc]; };
   CellBench = derive2 { name="CellBench"; version="1.14.0"; sha256="0p5bs7v5ya31z0hxaw52ccx8qv8yq86q6k0qcd2z20fia0f9471v"; depends=[BiocFileCache BiocGenerics BiocParallel dplyr glue lubridate magrittr memoise purrr rappdirs rlang SingleCellExperiment tibble tidyr tidyselect]; };
   CellMapper = derive2 { name="CellMapper"; version="1.24.0"; sha256="172bmzk5g18slvym5w557c9wy7irb0mp81kanwn1csk0va3cl9pc"; depends=[S4Vectors]; };
@@ -202,13 +202,13 @@ in with self; {
   CellScore = derive2 { name="CellScore"; version="1.18.0"; sha256="1790p98zhjl3lpm4xcn3rjwizmzgpylzk7c0ndn5hlrz5ck3qmbm"; depends=[Biobase gplots lsa RColorBrewer squash]; };
   CellTrails = derive2 { name="CellTrails"; version="1.16.0"; sha256="02jwp5ypp32hs8sxgi8ifv62sadlpgd8g8i6i03yahwz7pd8d3ry"; depends=[Biobase BiocGenerics cba dendextend dtw EnvStats ggplot2 ggrepel igraph maptree mgcv reshape2 Rtsne SingleCellExperiment SummarizedExperiment]; };
   CellaRepertorium = derive2 { name="CellaRepertorium"; version="1.8.0"; sha256="144d1h73x4gbymjka5a4i5nvqj7fmmhw9kdq1a9qmf0bah2xwcv0"; depends=[BiocGenerics Biostrings dplyr forcats generics glue Matrix progress purrr Rcpp reshape2 rlang S4Vectors stringr tibble tidyr]; };
-  CelliD = derive2 { name="CelliD"; version="1.6.0"; sha256="1qg14d4fv2wbwcs0gsw0vvn3lny9sdk3k1ybxci8sd847r7jrahm"; depends=[BiocParallel data_table fastmatch fgsea ggplot2 glue irlba Matrix matrixStats pbapply Rcpp RcppArmadillo reticulate Rtsne scater Seurat SingleCellExperiment stringr SummarizedExperiment tictoc umap]; };
+  CelliD = derive2 { name="CelliD"; version="1.6.2"; sha256="0dh9nn8kx6fsiqjakm2abx9cz19ppqz8c0wly5lhj54gfnmri7gc"; depends=[BiocParallel data_table fastmatch fgsea ggplot2 glue irlba Matrix matrixStats pbapply Rcpp RcppArmadillo reticulate Rtsne scater Seurat SingleCellExperiment stringr SummarizedExperiment tictoc umap]; };
   Cepo = derive2 { name="Cepo"; version="1.4.0"; sha256="07ymk3kw0r8sdk3fyssh93ap3fx2xq5mhznksdvi2i1k4rv2pc07"; depends=[BiocParallel DelayedArray DelayedMatrixStats dplyr ggplot2 GSEABase HDF5Array patchwork reshape2 rlang S4Vectors SingleCellExperiment SummarizedExperiment]; };
   CexoR = derive2 { name="CexoR"; version="1.36.0"; sha256="0bd3kd3d67h3wbp7wbccwqppm3pfmvb45k4k13w772mawzr2k6ja"; depends=[genomation GenomeInfoDb GenomicRanges idr IRanges RColorBrewer Rsamtools rtracklayer S4Vectors]; };
   ChAMP = derive2 { name="ChAMP"; version="2.28.0"; sha256="10ss0a3miqrx92vy1r1h5rv3mnjn4iyl32q86s0x59d3fvqp2cx1"; 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="1.18.0"; sha256="1z00d2952qwscx5ljr7zvxm6kydmk188iiky0zprxl9hzp69iv17"; depends=[BiocGenerics caret caTools ChIC_data genomeIntervals GenomicRanges IRanges progress randomForest Rsamtools S4Vectors]; };
   ChIPComp = derive2 { name="ChIPComp"; version="1.28.0"; sha256="1wnc7zrnnxk3nlk2l9y4il75dzirndp4vs5ivxn5rzqr6p7h4bhw"; depends=[BiocGenerics BSgenome_Hsapiens_UCSC_hg19 BSgenome_Mmusculus_UCSC_mm9 GenomeInfoDb GenomicRanges IRanges limma Rsamtools rtracklayer S4Vectors]; };
-  ChIPQC = derive2 { name="ChIPQC"; version="1.34.0"; sha256="1kkrr0i30m1mnp274db2q9rwrgsrc4659smck62r07k8dympdhk8"; 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="1.34.1"; sha256="18kggxvmjjgnkgyx6p7l5n3f7v5smqyamg91b1jp204i8idmw3a9"; 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="1.42.0"; sha256="06yg5fvq0z63iz9jfpjl4bd5bzppz8ai9j3am1m5h1632xdlp3bh"; depends=[affy biganalytics bigmemory Biobase ChIPXpressData frma GEOquery]; };
   ChIPanalyser = derive2 { name="ChIPanalyser"; version="1.20.0"; sha256="04gdhzvhqnq2w0dcx2153bkg2ywrmz2zjg323sajl1gm32dn036g"; depends=[BiocManager Biostrings BSgenome GenomeInfoDb GenomicRanges IRanges RColorBrewer RcppRoll ROCR rtracklayer S4Vectors]; };
   ChIPexoQual = derive2 { name="ChIPexoQual"; version="1.22.0"; sha256="0k4vbdwpp7z06fzjgqnmrx2yllayc0z2baj26bh4vji5vb48k9ik"; depends=[BiocParallel biovizBase broom data_table dplyr GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 hexbin IRanges RColorBrewer rmarkdown Rsamtools S4Vectors scales viridis]; };
@@ -223,7 +223,7 @@ in with self; {
   ChromSCape = derive2 { name="ChromSCape"; version="1.8.0"; sha256="0zvvc826zqi88gr2m4lzgmc2mgh83f9vc6f033l77a367v7p5cnk"; 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="1.0.0"; sha256="0jc63nmlkvx829h85fk8wh9sma200hv0g3a94slxhdiidnjph7l6"; depends=[BiocGenerics Biostrings dplyr ggplot2 IRanges magrittr Rbowtie2 Rhisat2 rlang Rsamtools S4Vectors ShortRead tidyr]; };
   CiteFuse = derive2 { name="CiteFuse"; version="1.10.0"; sha256="04zf5bvwqgr8rk4mzdglrbys62qsqgm4d5yzn2gpyk74qb8jcbir"; depends=[cowplot dbscan ggplot2 ggraph ggridges gridExtra igraph Matrix mixtools pheatmap randomForest reshape2 rhdf5 rlang Rtsne S4Vectors scales scran SingleCellExperi