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{
"R": {
"Version": "4.5.0",
"Repositories": [
{
"Name": "BioCsoft",
"URL": "https://bioconductor.org/packages/3.21/bioc"
},
{
"Name": "BioCann",
"URL": "https://bioconductor.org/packages/3.21/data/annotation"
},
{
"Name": "BioCexp",
"URL": "https://bioconductor.org/packages/3.21/data/experiment"
},
{
"Name": "BioCworkflows",
"URL": "https://bioconductor.org/packages/3.21/workflows"
},
{
"Name": "BioCbooks",
"URL": "https://bioconductor.org/packages/3.21/books"
},
{
"Name": "CRAN",
"URL": "https://cloud.r-project.org"
}
]
},
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"Version": "3.21"
},
"Packages": {
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"Package": "Biobase",
"Version": "2.68.0",
"Source": "Bioconductor",
"Title": "Biobase: Base functions for Bioconductor",
"Description": "Functions that are needed by many other packages or which replace R functions.",
"biocViews": "Infrastructure",
"URL": "https://bioconductor.org/packages/Biobase",
"BugReports": "https://github.com/Bioconductor/Biobase/issues",
"License": "Artistic-2.0",
"Authors@R": "c( person(\"R.\", \"Gentleman\", role=\"aut\"), person(\"V.\", \"Carey\", role = \"aut\"), person(\"M.\", \"Morgan\", role=\"aut\"), person(\"S.\", \"Falcon\", role=\"aut\"), person(\"Haleema\", \"Khan\", role = \"ctb\", comment = \"'esApply' and 'BiobaseDevelopment' vignette translation from Sweave to Rmarkdown / HTML\" ), person(\"Bioconductor Package Maintainer\", role = \"cre\", email = \"maintainer@bioconductor.org\" ))",
"Suggests": [
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"ALL",
"RUnit",
"golubEsets",
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"knitr",
"limma"
],
"Depends": [
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"BiocGenerics (>= 0.27.1)",
"utils"
],
"Imports": [
"methods"
],
"VignetteBuilder": "knitr",
"LazyLoad": "yes",
"Collate": "tools.R strings.R environment.R vignettes.R packages.R AllGenerics.R VersionsClass.R VersionedClasses.R methods-VersionsNull.R methods-VersionedClass.R DataClasses.R methods-aggregator.R methods-container.R methods-MIAxE.R methods-MIAME.R methods-AssayData.R methods-AnnotatedDataFrame.R methods-eSet.R methods-ExpressionSet.R methods-MultiSet.R methods-SnpSet.R methods-NChannelSet.R anyMissing.R rowOp-methods.R updateObjectTo.R methods-ScalarObject.R zzz.R",
"git_url": "https://git.bioconductor.org/packages/Biobase",
"git_branch": "RELEASE_3_21",
"git_last_commit": "9fd33ea",
"git_last_commit_date": "2025-04-15",
"Repository": "Bioconductor 3.21",
"NeedsCompilation": "yes",
"Author": "R. Gentleman [aut], V. Carey [aut], M. Morgan [aut], S. Falcon [aut], Haleema Khan [ctb] ('esApply' and 'BiobaseDevelopment' vignette translation from Sweave to Rmarkdown / HTML), Bioconductor Package Maintainer [cre]",
"Maintainer": "Bioconductor Package Maintainer <maintainer@bioconductor.org>"
},
"BiocBaseUtils": {
"Package": "BiocBaseUtils",
"Version": "1.10.0",
"Source": "Bioconductor",
"Title": "General utility functions for developing Bioconductor packages",
"Authors@R": "c( person(\"Marcel\", \"Ramos\", , \"marcel.ramos@sph.cuny.edu\", c(\"aut\", \"cre\"), c(ORCID = \"0000-0002-3242-0582\") ), person(\"Martin\", \"Morgan\", , \"martin.morgan@roswellpark.org\", \"ctb\" ), person(\"Hervé\", \"Pagès\", , \"hpages.on.github@gmail.com\", \"ctb\") )",
"Description": "The package provides utility functions related to package development. These include functions that replace slots, and selectors for show methods. It aims to coalesce the various helper functions often re-used throughout the Bioconductor ecosystem.",
"Imports": [
"methods",
"utils"
],
"Depends": [
"R (>= 4.2.0)"
],
"Suggests": [
"knitr",
"rmarkdown",
"BiocStyle",
"tinytest"
],
"License": "Artistic-2.0",
"Encoding": "UTF-8",
"biocViews": "Software, Infrastructure",
"BugReports": "https://www.github.com/Bioconductor/BiocBaseUtils/issues",
"Roxygen": "list(markdown = TRUE)",
"RoxygenNote": "7.3.2",
"VignetteBuilder": "knitr",
"Date": "2024-08-22",
"git_url": "https://git.bioconductor.org/packages/BiocBaseUtils",
"git_branch": "RELEASE_3_21",
"git_last_commit": "af524da",
"git_last_commit_date": "2025-04-15",
"Repository": "Bioconductor 3.21",
"NeedsCompilation": "no",
"Author": "Marcel Ramos [aut, cre] (ORCID: <https://orcid.org/0000-0002-3242-0582>), Martin Morgan [ctb], Hervé Pagès [ctb]",
"Maintainer": "Marcel Ramos <marcel.ramos@sph.cuny.edu>"
},
"BiocGenerics": {
"Package": "BiocGenerics",
"Version": "0.54.0",
"Source": "Bioconductor",
"Title": "S4 generic functions used in Bioconductor",
"Description": "The package defines many S4 generic functions used in Bioconductor.",
"biocViews": "Infrastructure",
"URL": "https://bioconductor.org/packages/BiocGenerics",
"BugReports": "https://github.com/Bioconductor/BiocGenerics/issues",
"License": "Artistic-2.0",
"Encoding": "UTF-8",
"Authors@R": "c( person(\"The Bioconductor Dev Team\", role=\"aut\"), person(\"Hervé\", \"Pagès\", role=c(\"aut\", \"cre\"), email=\"hpages.on.github@gmail.com\", comment=c(ORCID=\"0009-0002-8272-4522\")), person(\"Laurent\", \"Gatto\", role=\"ctb\", email=\"laurent.gatto@uclouvain.be\", comment=c(ORCID=\"0000-0002-1520-2268\")), person(\"Nathaniel\", \"Hayden\", role=\"ctb\"), person(\"James\", \"Hester\", role=\"ctb\"), person(\"Wolfgang\", \"Huber\", role=\"ctb\"), person(\"Michael\", \"Lawrence\", role=\"ctb\"), person(\"Martin\", \"Morgan\", role=\"ctb\", email=\"mtmorgan.xyz@gmail.com\", comment=c(ORCID=\"0000-0002-5874-8148\")), person(\"Valerie\", \"Obenchain\", role=\"ctb\"))",
"Depends": [
"R (>= 4.0.0)",
"methods",
"utils",
"graphics",
"stats",
"generics"
],
"Imports": [
"methods",
"utils",
"graphics",
"stats"
],
"Suggests": [
"Biobase",
"S4Vectors",
"IRanges",
"S4Arrays",
"SparseArray",
"DelayedArray",
"HDF5Array",
"GenomicRanges",
"pwalign",
"Rsamtools",
"AnnotationDbi",
"affy",
"affyPLM",
"DESeq2",
"flowClust",
"MSnbase",
"annotate",
"MultiAssayExperiment",
"RUnit"
],
"Collate": "S3-classes-as-S4-classes.R utils.R normarg-utils.R replaceSlots.R aperm.R append.R as.data.frame.R as.list.R as.vector.R cbind.R do.call.R duplicated.R eval.R Extremes.R format.R funprog.R get.R grep.R is.unsorted.R lapply.R mapply.R match.R mean.R nrow.R order.R paste.R rank.R rep.R row_colnames.R saveRDS.R sort.R start.R subset.R t.R table.R tapply.R unique.R unlist.R unsplit.R which.R which.min.R relist.R boxplot.R image.R density.R IQR.R mad.R residuals.R var.R weights.R xtabs.R setops.R annotation.R combine.R containsOutOfMemoryData.R dbconn.R dge.R dims.R fileName.R longForm.R normalize.R Ontology.R organism_species.R paste2.R path.R plotMA.R plotPCA.R score.R strand.R toTable.R type.R updateObject.R testPackage.R zzz.R",
"git_url": "https://git.bioconductor.org/packages/BiocGenerics",
"git_branch": "RELEASE_3_21",
"git_last_commit": "75c4815",
"git_last_commit_date": "2025-04-15",
"Repository": "Bioconductor 3.21",
"NeedsCompilation": "no",
"Author": "The Bioconductor Dev Team [aut], Hervé Pagès [aut, cre] (ORCID: <https://orcid.org/0009-0002-8272-4522>), Laurent Gatto [ctb] (ORCID: <https://orcid.org/0000-0002-1520-2268>), Nathaniel Hayden [ctb], James Hester [ctb], Wolfgang Huber [ctb], Michael Lawrence [ctb], Martin Morgan [ctb] (ORCID: <https://orcid.org/0000-0002-5874-8148>), Valerie Obenchain [ctb]",
"Maintainer": "Hervé Pagès <hpages.on.github@gmail.com>"
},
"BiocManager": {
"Package": "BiocManager",
"Version": "1.30.25",
"Source": "Repository",
"Title": "Access the Bioconductor Project Package Repository",
"Description": "A convenient tool to install and update Bioconductor packages.",
"Authors@R": "c( person(\"Martin\", \"Morgan\", email = \"martin.morgan@roswellpark.org\", role = \"aut\", comment = c(ORCID = \"0000-0002-5874-8148\")), person(\"Marcel\", \"Ramos\", email = \"marcel.ramos@sph.cuny.edu\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-3242-0582\")))",
"Imports": [
"utils"
],
"Suggests": [
"BiocVersion",
"BiocStyle",
"remotes",
"rmarkdown",
"testthat",
"withr",
"curl",
"knitr"
],
"URL": "https://bioconductor.github.io/BiocManager/",
"BugReports": "https://github.com/Bioconductor/BiocManager/issues",
"VignetteBuilder": "knitr",
"License": "Artistic-2.0",
"Encoding": "UTF-8",
"RoxygenNote": "7.3.1",
"NeedsCompilation": "no",
"Author": "Martin Morgan [aut] (<https://orcid.org/0000-0002-5874-8148>), Marcel Ramos [aut, cre] (<https://orcid.org/0000-0002-3242-0582>)",
"Maintainer": "Marcel Ramos <marcel.ramos@sph.cuny.edu>",
"Repository": "CRAN"
},
"BiocVersion": {
"Package": "BiocVersion",
"Version": "3.21.1",
"Source": "Bioconductor",
"Title": "Set the appropriate version of Bioconductor packages",
"Description": "This package provides repository information for the appropriate version of Bioconductor.",
"Authors@R": "c( person(\"Martin\", \"Morgan\", email = \"martin.morgan@roswellpark.org\", role = \"aut\"), person(\"Marcel\", \"Ramos\", email = \"marcel.ramos@sph.cuny.edu\", role = \"ctb\"), person(\"Bioconductor\", \"Package Maintainer\", email = \"maintainer@bioconductor.org\", role = c(\"ctb\", \"cre\")))",
"biocViews": "Infrastructure",
"Depends": [
"R (>= 4.5.0)"
],
"License": "Artistic-2.0",
"Encoding": "UTF-8",
"RoxygenNote": "6.0.1",
"git_url": "https://git.bioconductor.org/packages/BiocVersion",
"git_branch": "devel",
"git_last_commit": "1e5e5af",
"git_last_commit_date": "2024-10-29",
"Repository": "Bioconductor 3.21",
"NeedsCompilation": "no",
"Author": "Martin Morgan [aut], Marcel Ramos [ctb], Bioconductor Package Maintainer [ctb, cre]",
"Maintainer": "Bioconductor Package Maintainer <maintainer@bioconductor.org>"
},
"DelayedArray": {
"Package": "DelayedArray",
"Version": "0.34.1",
"Source": "Bioconductor",
"Title": "A unified framework for working transparently with on-disk and in-memory array-like datasets",
"Description": "Wrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, ordinary arrays and, data frames.",
"biocViews": "Infrastructure, DataRepresentation, Annotation, GenomeAnnotation",
"URL": "https://bioconductor.org/packages/DelayedArray",
"BugReports": "https://github.com/Bioconductor/DelayedArray/issues",
"License": "Artistic-2.0",
"Encoding": "UTF-8",
"Authors@R": "c( person(\"Hervé\", \"Pagès\", role=c(\"aut\", \"cre\"), email=\"hpages.on.github@gmail.com\"), person(\"Aaron\", \"Lun\", role=\"ctb\", email=\"infinite.monkeys.with.keyboards@gmail.com\"), person(\"Peter\", \"Hickey\", role=\"ctb\", email=\"peter.hickey@gmail.com\"))",
"Maintainer": "Hervé Pagès <hpages.on.github@gmail.com>",
"Depends": [
"R (>= 4.0.0)",
"methods",
"stats4",
"Matrix",
"BiocGenerics (>= 0.53.3)",
"MatrixGenerics (>= 1.1.3)",
"S4Vectors (>= 0.27.2)",
"IRanges (>= 2.17.3)",
"S4Arrays (>= 1.5.4)",
"SparseArray (>= 1.7.5)"
],
"Imports": [
"stats"
],
"LinkingTo": [
"S4Vectors"
],
"Suggests": [
"BiocParallel",
"HDF5Array (>= 1.17.12)",
"genefilter",
"SummarizedExperiment",
"airway",
"lobstr",
"DelayedMatrixStats",
"knitr",
"rmarkdown",
"BiocStyle",
"RUnit"
],
"VignetteBuilder": "knitr",
"Collate": "compress_atomic_vector.R SparseArraySeed-class.R SparseArraySeed-utils.R read_sparse_block.R makeCappedVolumeBox.R AutoBlock-global-settings.R AutoGrid.R blockApply.R DelayedOp-class.R DelayedSubset-class.R DelayedAperm-class.R DelayedUnaryIsoOpStack-class.R DelayedUnaryIsoOpWithArgs-class.R DelayedSubassign-class.R DelayedSetDimnames-class.R DelayedNaryIsoOp-class.R DelayedAbind-class.R showtree.R simplify.R DelayedArray-class.R DelayedArray-subsetting.R chunkGrid.R RealizationSink-class.R realize.R DelayedArray-utils.R DelayedArray-stats.R matrixStats-methods.R DelayedMatrix-rowsum.R DelayedMatrix-mult.R ConstantArray-class.R RleArraySeed-class.R RleArray-class.R compat.R zzz.R",
"git_url": "https://git.bioconductor.org/packages/DelayedArray",
"git_branch": "RELEASE_3_21",
"git_last_commit": "93033ab",
"git_last_commit_date": "2025-04-17",
"Repository": "Bioconductor 3.21",
"NeedsCompilation": "yes",
"Author": "Hervé Pagès [aut, cre], Aaron Lun [ctb], Peter Hickey [ctb]"
},
"GenomeInfoDb": {
"Package": "GenomeInfoDb",
"Version": "1.44.0",
"Source": "Bioconductor",
"Title": "Utilities for manipulating chromosome names, including modifying them to follow a particular naming style",
"Description": "Contains data and functions that define and allow translation between different chromosome sequence naming conventions (e.g., \"chr1\" versus \"1\"), including a function that attempts to place sequence names in their natural, rather than lexicographic, order.",
"biocViews": "Genetics, DataRepresentation, Annotation, GenomeAnnotation",
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