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jayhesselberthjayhesselberth
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Add new packages to renv
Not sure why bioc is being downgraded to 3.20 in the top-level lock file, but the package versions are current with 3.21
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‎renv.lock‎

Lines changed: 263 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -4,23 +4,23 @@
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"Repositories": [
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{
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"Name": "BioCsoft",
7-
"URL": "https://bioconductor.org/packages/3.21/bioc"
7+
"URL": "https://bioconductor.org/packages/3.20/bioc"
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},
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{
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"Name": "BioCann",
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"URL": "https://bioconductor.org/packages/3.21/data/annotation"
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"URL": "https://bioconductor.org/packages/3.20/data/annotation"
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},
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{
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"Name": "BioCexp",
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"URL": "https://bioconductor.org/packages/3.21/data/experiment"
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"URL": "https://bioconductor.org/packages/3.20/data/experiment"
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},
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{
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"Name": "BioCworkflows",
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"URL": "https://bioconductor.org/packages/3.21/workflows"
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"URL": "https://bioconductor.org/packages/3.20/workflows"
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},
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{
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"Name": "BioCbooks",
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"URL": "https://bioconductor.org/packages/3.21/books"
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"URL": "https://bioconductor.org/packages/3.20/books"
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},
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{
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"Name": "CRAN",
@@ -127,6 +127,75 @@
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"Author": "Martin Morgan [aut], Johannes Rainer [aut], Joachim Bargsten [ctb], Daniel Van Twisk [ctb], Bioconductor Package Maintainer [cre]",
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"Maintainer": "Bioconductor Package Maintainer <maintainer@bioconductor.org>"
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},
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"AnnotationHub": {
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"Package": "AnnotationHub",
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"Version": "3.16.1",
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"Source": "Bioconductor",
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"Type": "Package",
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"Title": "Client to access AnnotationHub resources",
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"Authors@R": "c(person(\"Bioconductor Package\", \"Maintainer\", email=\"maintainer@bioconductor.org\", role=\"cre\"), person(\"Martin\", \"Morgan\", role=\"aut\"), person(\"Marc\", \"Carlson\", role=\"ctb\"), person(\"Dan\", \"Tenenbaum\", role=\"ctb\"), person(\"Sonali\", \"Arora\", role=\"ctb\"), person(\"Valerie\", \"Oberchain\", role=\"ctb\"), person(\"Kayla\", \"Morrell\", role=\"ctb\"), person(\"Lori\", \"Shepherd\", role=\"aut\"))",
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"biocViews": "Infrastructure, DataImport, GUI, ThirdPartyClient",
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"Description": "This package provides a client for the Bioconductor AnnotationHub web resource. The AnnotationHub web resource provides a central location where genomic files (e.g., VCF, bed, wig) and other resources from standard locations (e.g., UCSC, Ensembl) can be discovered. The resource includes metadata about each resource, e.g., a textual description, tags, and date of modification. The client creates and manages a local cache of files retrieved by the user, helping with quick and reproducible access.",
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"License": "Artistic-2.0",
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"Depends": [
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"BiocGenerics (>= 0.15.10)",
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"BiocFileCache (>= 1.5.1)"
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],
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"Imports": [
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"utils",
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"methods",
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"grDevices",
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"RSQLite",
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"BiocManager",
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"BiocVersion",
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"curl",
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"rappdirs",
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"AnnotationDbi (>= 1.31.19)",
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"S4Vectors",
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"httr",
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"yaml",
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"dplyr"
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],
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"Suggests": [
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"IRanges",
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"GenomicRanges",
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"GenomeInfoDb",
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"VariantAnnotation",
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"Rsamtools",
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"rtracklayer",
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"BiocStyle",
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"knitr",
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"AnnotationForge",
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"rBiopaxParser",
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"RUnit",
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"txdbmaker",
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"MSnbase",
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"mzR",
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"Biostrings",
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"CompoundDb",
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"keras",
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"ensembldb",
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"SummarizedExperiment",
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"ExperimentHub",
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"gdsfmt",
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"rmarkdown",
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"HubPub"
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],
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"Enhances": [
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"AnnotationHubData"
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],
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"Collate": "AnnotationHubOption.R AllGenerics.R Hub-class.R db-utils.R AnnotationHub-class.R AnnotationHubResource-class.R BEDResource-class.R ProteomicsResource-class.R EpigenomeResource-class.R EnsDbResource-class.R utilities.R sql-utils.R Hub-utils.R cache-utils.R zzz.R",
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"VignetteBuilder": "knitr",
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"BugReports": "https://github.com/Bioconductor/AnnotationHub/issues",
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"NeedsCompilation": "yes",
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"git_url": "https://git.bioconductor.org/packages/AnnotationHub",
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"git_branch": "RELEASE_3_21",
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"git_last_commit": "cda9c0e",
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"git_last_commit_date": "2025-07-17",
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"Repository": "Bioconductor 3.21",
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"Author": "Bioconductor Package Maintainer [cre], Martin Morgan [aut], Marc Carlson [ctb], Dan Tenenbaum [ctb], Sonali Arora [ctb], Valerie Oberchain [ctb], Kayla Morrell [ctb], Lori Shepherd [aut]",
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"Maintainer": "Bioconductor Package Maintainer <maintainer@bioconductor.org>"
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},
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"BH": {
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"Package": "BH",
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"Version": "1.87.0-1",
@@ -203,6 +272,32 @@
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"Author": "Hervé Pagès [aut, cre]",
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"Maintainer": "Hervé Pagès <hpages.on.github@gmail.com>"
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},
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"BSgenome.Hsapiens.UCSC.hg19": {
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"Package": "BSgenome.Hsapiens.UCSC.hg19",
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"Version": "1.4.3",
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"Source": "Bioconductor",
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"Title": "Full genome sequences for Homo sapiens (UCSC version hg19, based on GRCh37.p13)",
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"Description": "Full genome sequences for Homo sapiens (Human) as provided by UCSC (hg19, based on GRCh37.p13) and stored in Biostrings objects.",
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"Author": "The Bioconductor Dev Team",
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"Maintainer": "Bioconductor Package Maintainer <maintainer@bioconductor.org>",
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"Depends": [
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"BSgenome (>= 1.54.0)"
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],
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"Imports": [
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"BSgenome"
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],
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"Suggests": [],
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"License": "Artistic-2.0",
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"organism": "Homo sapiens",
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"common_name": "Human",
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"provider": "UCSC",
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"provider_version": "hg19",
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"release_date": "June 2013",
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"release_name": "Genome Reference Consortium GRCh37.p13",
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"source_url": "https://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/latest/",
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"biocViews": "AnnotationData, Genetics, BSgenome, Homo_sapiens",
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"NeedsCompilation": "no"
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},
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"BSgenome.Scerevisiae.UCSC.sacCer3": {
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"Package": "BSgenome.Scerevisiae.UCSC.sacCer3",
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"Version": "1.4.0",
@@ -2500,6 +2595,30 @@
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"Author": "Martin Morgan [aut], Valerie Obenchain [aut], Jim Hester [aut], Hervé Pagès [aut, cre]",
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"Maintainer": "Hervé Pagès <hpages.on.github@gmail.com>"
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},
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"TxDb.Hsapiens.UCSC.hg19.knownGene": {
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"Package": "TxDb.Hsapiens.UCSC.hg19.knownGene",
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"Version": "3.2.2",
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"Source": "Bioconductor",
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"Title": "Annotation package for TxDb object(s)",
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"Description": "Exposes an annotation databases generated from UCSC by exposing these as TxDb objects",
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"Author": "Marc Carlson, Bioconductor Package Maintainer <maintainer@bioconductor.org> [cre]",
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"Maintainer": "Bioconductor Package Maintainer <maintainer@bioconductor.org>",
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"Depends": [
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"GenomicFeatures (>= 1.21.30)"
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],
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"Imports": [
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"AnnotationDbi"
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],
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"License": "Artistic-2.0",
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"organism": "Homo sapiens",
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"species": "Homo sapiens",
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"provider": "UCSC",
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"provider_version": "hg19 genome based on the knownGene table",
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"release_date": "2015-10-07 18:11:28 +0000 (Wed, 07 Oct 2015)",
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"resource_url": "http://genome.ucsc.edu/",
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"biocViews": "AnnotationData, Genetics, TxDb, Homo_sapiens",
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"NeedsCompilation": "no"
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},
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"TxDb.Scerevisiae.UCSC.sacCer3.sgdGene": {
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"Package": "TxDb.Scerevisiae.UCSC.sacCer3.sgdGene",
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"Version": "3.2.2",
@@ -2762,6 +2881,73 @@
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"Author": "Tony Plate [aut, cre], Richard Heiberger [aut]",
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"Repository": "CRAN"
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},
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"annotatr": {
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"Package": "annotatr",
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"Version": "1.34.0",
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"Source": "Bioconductor",
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"Title": "Annotation of Genomic Regions to Genomic Annotations",
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"Date": "2021-11-20",
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"Authors@R": "c( person(\"Raymond G.\", \"Cavalcante\", email = \"rcavalca@umich.edu\", role = c(\"aut\", \"cre\")), person(c(\"Maureen A.\"), \"Sartor\", email = \"sartorma@med.umich.edu\", role = c(\"ths\")))",
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"Description": "Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs, differentially methylated CpGs or regions, SNPs, etc.) it is often of interest to investigate the intersecting genomic annotations. Such annotations include those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs), CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as enhancers. The annotatr package provides an easy way to summarize and visualize the intersection of genomic sites/regions with genomic annotations.",
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"Depends": [
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"R (>= 3.5.0)"
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],
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"Imports": [
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"AnnotationDbi",
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"AnnotationHub",
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"dplyr",
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"GenomicFeatures",
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"GenomicRanges",
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"GenomeInfoDb (>= 1.10.3)",
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"ggplot2",
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"IRanges",
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"methods",
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"readr",
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"regioneR",
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"reshape2",
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"rtracklayer",
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"S4Vectors (>= 0.23.10)",
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"stats",
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"utils"
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],
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"Suggests": [
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"BiocStyle",
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"devtools",
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"knitr",
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"org.Dm.eg.db",
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"org.Gg.eg.db",
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"org.Hs.eg.db",
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"org.Mm.eg.db",
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"org.Rn.eg.db",
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"rmarkdown",
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"roxygen2",
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"testthat",
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"TxDb.Dmelanogaster.UCSC.dm3.ensGene",
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"TxDb.Dmelanogaster.UCSC.dm6.ensGene",
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"TxDb.Ggallus.UCSC.galGal5.refGene",
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"TxDb.Hsapiens.UCSC.hg19.knownGene",
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"TxDb.Hsapiens.UCSC.hg38.knownGene",
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"TxDb.Mmusculus.UCSC.mm9.knownGene",
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"TxDb.Mmusculus.UCSC.mm10.knownGene",
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"TxDb.Rnorvegicus.UCSC.rn4.ensGene",
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"TxDb.Rnorvegicus.UCSC.rn5.refGene",
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"TxDb.Rnorvegicus.UCSC.rn6.refGene"
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],
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"VignetteBuilder": "knitr",
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"BugReports": "https://www.github.com/rcavalcante/annotatr/issues",
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"License": "GPL-3",
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"LazyData": "true",
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"RoxygenNote": "7.1.2",
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"biocViews": "Software, Annotation, GenomeAnnotation, FunctionalGenomics, Visualization",
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"git_url": "https://git.bioconductor.org/packages/annotatr",
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"git_branch": "RELEASE_3_21",
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"git_last_commit": "a16eede",
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"git_last_commit_date": "2025-04-15",
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"Repository": "Bioconductor 3.21",
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"NeedsCompilation": "no",
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"Author": "Raymond G. Cavalcante [aut, cre], Maureen A. Sartor [ths]",
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"Maintainer": "Raymond G. Cavalcante <rcavalca@umich.edu>"
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},
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"ape": {
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"Package": "ape",
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"Version": "5.8-1",
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"Maintainer": "Jeroen Ooms <jeroenooms@gmail.com>",
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"Repository": "CRAN"
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},
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"org.Hs.eg.db": {
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"Package": "org.Hs.eg.db",
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"Version": "3.21.0",
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"Source": "Bioconductor",
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"Title": "Genome wide annotation for Human",
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"Description": "Genome wide annotation for Human, primarily based on mapping using Entrez Gene identifiers.",
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"Author": "Marc Carlson",
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"Maintainer": "Bioconductor Package Maintainer <maintainer@bioconductor.org>",
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"Depends": [
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"R (>= 2.7.0)",
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"methods",
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"AnnotationDbi (>= 1.69.0)"
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],
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"Suggests": [
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"DBI",
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"annotate",
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"RUnit"
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],
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"License": "Artistic-2.0",
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"organism": "Homo sapiens",
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"species": "Human",
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"biocViews": "OrgDb, AnnotationData, Homo_sapiens, humanLLMappings",
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"NeedsCompilation": "no"
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},
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"pak": {
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"Package": "pak",
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"Version": "0.9.0",
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"Maintainer": "Ben Bolker <bolker@mcmaster.ca>",
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"Repository": "CRAN"
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},
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"regioneR": {
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"Package": "regioneR",
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"Version": "1.40.1",
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"Source": "Bioconductor",
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"Type": "Package",
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"Title": "Association analysis of genomic regions based on permutation tests",
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"Date": "2018-08-14",
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"Author": "Anna Diez-Villanueva <adiez@iconcologia.net>, Roberto Malinverni <roberto.malinverni@gmail.com> and Bernat Gel <bgel@igtp.cat>",
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"Maintainer": "Bernat Gel <bgel@imppc.org>",
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"Description": "regioneR offers a statistical framework based on customizable permutation tests to assess the association between genomic region sets and other genomic features.",
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"License": "Artistic-2.0",
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"Depends": [
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"GenomicRanges"
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],
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"Imports": [
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"memoise",
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"GenomicRanges",
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"IRanges",
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"BSgenome",
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"Biostrings",
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"rtracklayer",
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"parallel",
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"graphics",
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"stats",
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"utils",
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"methods",
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"GenomeInfoDb",
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"S4Vectors",
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"tools"
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],
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"Suggests": [
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"BiocStyle",
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"knitr",
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"rmarkdown",
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"BSgenome.Hsapiens.UCSC.hg19.masked",
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"testthat"
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],
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"VignetteBuilder": "knitr",
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"Encoding": "UTF-8",
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"biocViews": "Genetics, ChIPSeq, DNASeq, MethylSeq, CopyNumberVariation",
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"NeedsCompilation": "no",
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"RoxygenNote": "7.2.1",
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"git_url": "https://git.bioconductor.org/packages/regioneR",
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"git_branch": "RELEASE_3_21",
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"git_last_commit": "9f9c28f",
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"git_last_commit_date": "2025-05-27",
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"Repository": "Bioconductor 3.21"
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},
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"rematch": {
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"Package": "rematch",
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"Version": "2.0.0",

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