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{
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"Name": "BioCsoft",
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{
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"License": "BSL-1.0",
"URL": "https://github.com/eddelbuettel/bh, https://dirk.eddelbuettel.com/code/bh.html",
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"Author": "Dirk Eddelbuettel [aut, cre] (<https://orcid.org/0000-0001-6419-907X>), John W. Emerson [aut], Michael J. Kane [aut] (<https://orcid.org/0000-0003-1899-6662>)",
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"Repository": "CRAN",
"Encoding": "UTF-8"
},
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"Title": "Biobase: Base functions for Bioconductor",
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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\" ))",
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],
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],
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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_20",
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"Repository": "Bioconductor 3.20",
"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]",
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"Title": "Manage Files Across Sessions",
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"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.",
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],
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],
"BugReports": "https://github.com/Bioconductor/BiocFileCache/issues",
"DevelopmentURL": "https://github.com/Bioconductor/BiocFileCache",
"License": "Artistic-2.0",
"Encoding": "UTF-8",
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"biocViews": "DataImport",
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],
"git_url": "https://git.bioconductor.org/packages/BiocFileCache",
"git_branch": "RELEASE_3_20",
"git_last_commit": "66862c5",
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"Repository": "Bioconductor 3.20",
"NeedsCompilation": "no",
"Author": "Lori Shepherd [aut, cre], Martin Morgan [aut]",
"Maintainer": "Lori Shepherd <lori.shepherd@roswellpark.org>"
},
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"Version": "0.52.0",
"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",
"Author": "The Bioconductor Dev Team",
"Maintainer": "Hervé Pagès <hpages.on.github@gmail.com>",
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"methods",
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],
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],
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"IRanges",
"S4Arrays",
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"GenomicRanges",
"pwalign",
"Rsamtools",
"AnnotationDbi",
"affy",
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"MSnbase",
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],
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"git_url": "https://git.bioconductor.org/packages/BiocGenerics",
"git_branch": "RELEASE_3_20",
"git_last_commit": "1422115",
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"Repository": "Bioconductor 3.20",
"NeedsCompilation": "no"
},
"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": [
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],
"Suggests": [
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"BiocStyle",
"remotes",
"rmarkdown",
"testthat",
"withr",
"curl",
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],
"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"
},
"BiocNeighbors": {
"Package": "BiocNeighbors",
"Version": "2.0.1",
"Source": "Bioconductor",
"Date": "2024-11-26",
"Title": "Nearest Neighbor Detection for Bioconductor Packages",
"Authors@R": "c(person(\"Aaron\", \"Lun\", role=c(\"aut\", \"cre\", \"cph\"), email=\"infinite.monkeys.with.keyboards@gmail.com\"))",
"Imports": [
"Rcpp",
"methods"
],
"Suggests": [
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"testthat",
"BiocStyle",
"knitr",
"rmarkdown"
],
"biocViews": "Clustering, Classification",
"Description": "Implements exact and approximate methods for nearest neighbor detection, in a framework that allows them to be easily switched within Bioconductor packages or workflows. Exact searches can be performed using the k-means for k-nearest neighbors algorithm or with vantage point trees. Approximate searches can be performed using the Annoy or HNSW libraries. Searching on either Euclidean or Manhattan distances is supported. Parallelization is achieved for all methods by using BiocParallel. Functions are also provided to search for all neighbors within a given distance.",
"License": "GPL-3",
"LinkingTo": [
"Rcpp",
"assorthead"
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