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{
"R": {
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{
"Name": "BioCsoft",
"URL": "https://bioconductor.org/packages/3.21/bioc"
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{
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"URL": "https://bioconductor.org/packages/3.21/data/annotation"
},
{
"Name": "BioCexp",
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},
{
"Name": "BioCworkflows",
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},
{
"Name": "BioCbooks",
"URL": "https://bioconductor.org/packages/3.21/books"
},
{
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}
]
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"URL": "https://bioconductor.org/packages/AnnotationDbi",
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"BugReports": "https://github.com/Bioconductor/AnnotationDbi/issues",
"License": "Artistic-2.0",
"Encoding": "UTF-8",
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],
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],
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"git_url": "https://git.bioconductor.org/packages/AnnotationDbi",
"git_branch": "RELEASE_3_21",
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"git_last_commit_date": "2025-04-15",
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},
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"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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],
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],
"Imports": [
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],
"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>"
},
"BiocFileCache": {
"Package": "BiocFileCache",
"Version": "2.16.0",
"Source": "Bioconductor",
"Title": "Manage Files Across Sessions",
"Authors@R": "c(person(\"Lori\", \"Shepherd\", email = \"lori.shepherd@roswellpark.org\", role = c(\"aut\", \"cre\")), person(\"Martin\", \"Morgan\", email = \"martin.morgan@roswellpark.org\", role = \"aut\"))",
"Description": "This package creates a persistent on-disk cache of files that the user can add, update, and retrieve. It is useful for managing resources (such as custom Txdb objects) that are costly or difficult to create, web resources, and data files used across sessions.",
"Depends": [
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"dbplyr (>= 1.0.0)"
],
"Imports": [
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"stats",
"utils",
"dplyr",
"RSQLite",
"DBI",
"filelock",
"curl",
"httr"
],
"BugReports": "https://github.com/Bioconductor/BiocFileCache/issues",
"DevelopmentURL": "https://github.com/Bioconductor/BiocFileCache",
"License": "Artistic-2.0",
"Encoding": "UTF-8",
"RoxygenNote": "7.3.2",
"biocViews": "DataImport",
"VignetteBuilder": "knitr",
"Suggests": [
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"knitr",
"BiocStyle",
"rmarkdown",
"rtracklayer"
],
"git_url": "https://git.bioconductor.org/packages/BiocFileCache",
"git_branch": "RELEASE_3_21",
"git_last_commit": "021ad4e",
"git_last_commit_date": "2025-04-15",
"Repository": "Bioconductor 3.21",
"NeedsCompilation": "no",
"Author": "Lori Shepherd [aut, cre], Martin Morgan [aut]",
"Maintainer": "Lori Shepherd <lori.shepherd@roswellpark.org>"
},
"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": "1.30.26",
"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": "7.3.2",
"NeedsCompilation": "no",
"Author": "Martin Morgan [aut] (ORCID: <https://orcid.org/0000-0002-5874-8148>), Marcel Ramos [aut, cre] (ORCID: <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>"
},
"Biostrings": {
"Package": "Biostrings",
"Version": "2.76.0",
"Source": "Bioconductor",
"Title": "Efficient manipulation of biological strings",
"Description": "Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences.",
"biocViews": "SequenceMatching, Alignment, Sequencing, Genetics, DataImport, DataRepresentation, Infrastructure",
"URL": "https://bioconductor.org/packages/Biostrings",
"BugReports": "https://github.com/Bioconductor/Biostrings/issues",
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"Source": "Repository",
"Title": "Seamless R and C++ Integration",
"Date": "2025-01-11",
"Authors@R": "c(person(\"Dirk\", \"Eddelbuettel\", role = c(\"aut\", \"cre\"), email = \"edd@debian.org\", comment = c(ORCID = \"0000-0001-6419-907X\")), person(\"Romain\", \"Francois\", role = \"aut\", comment = c(ORCID = \"0000-0002-2444-4226\")), person(\"JJ\", \"Allaire\", role = \"aut\", comment = c(ORCID = \"0000-0003-0174-9868\")), person(\"Kevin\", \"Ushey\", role = \"aut\", comment = c(ORCID = \"0000-0003-2880-7407\")), person(\"Qiang\", \"Kou\", role = \"aut\", comment = c(ORCID = \"0000-0001-6786-5453\")), person(\"Nathan\", \"Russell\", role = \"aut\"), person(\"Iñaki\", \"Ucar\", role = \"aut\", comment = c(ORCID = \"0000-0001-6403-5550\")), person(\"Doug\", \"Bates\", role = \"aut\", comment = c(ORCID = \"0000-0001-8316-9503\")), person(\"John\", \"Chambers\", role = \"aut\"))",
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"Version": "14.4.3-1",
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"Title": "'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra Library",
"Date": "2025-05-21",
"Authors@R": "c(person(\"Dirk\", \"Eddelbuettel\", role = c(\"aut\", \"cre\"), email = \"edd@debian.org\", comment = c(ORCID = \"0000-0001-6419-907X\")), person(\"Romain\", \"Francois\", role = \"aut\", comment = c(ORCID = \"0000-0002-2444-4226\")), person(\"Doug\", \"Bates\", role = \"aut\", comment = c(ORCID = \"0000-0001-8316-9503\")), person(\"Binxiang\", \"Ni\", role = \"aut\"), person(\"Conrad\", \"Sanderson\", role = \"aut\", comment = c(ORCID = \"0000-0002-0049-4501\")))",
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"Source": "Repository",
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"Title": "'Rcpp' Integration for the 'Eigen' Templated Linear Algebra Library",
"Date": "2024-08-23",
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"Copyright": "See the file COPYRIGHTS for various Eigen copyright details",
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"License": "GPL (>= 2) | file LICENSE",
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"Description": "A new object oriented programming system designed to be a successor to S3 and S4. It includes formal class, generic, and method specification, and a limited form of multiple dispatch. It has been designed and implemented collaboratively by the R Consortium Object-Oriented Programming Working Group, which includes representatives from R-Core, 'Bioconductor', 'Posit'/'tidyverse', and the wider R community.",
"License": "MIT + file LICENSE",
"URL": "https://rconsortium.github.io/S7/, https://github.com/RConsortium/S7",
"BugReports": "https://github.com/RConsortium/S7/issues",
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