{
  "_id": "6a1ac43d1d7bb097a09db1c7",
  "Package": "methylGSA",
  "Type": "Package",
  "Title": "Gene Set Analysis Using the Outcome of Differential Methylation",
  "Version": "1.31.0",
  "Authors@R": "c(\nperson(\"Xu\", \"Ren\",\nemail = \"xuren2120@gmail.com\", role = c(\"aut\", \"cre\")),\nperson(\"Pei Fen\", \"Kuan\",\nemail = \"peifen.kuan@stonybrook.edu\", role = \"aut\"))",
  "Description": "The main functions for methylGSA are methylglm and\nmethylRRA. methylGSA implements logistic regression adjusting\nnumber of probes as a covariate. methylRRA adjusts multiple\np-values of each gene by Robust Rank Aggregation. For more\ndetailed help information, please see the vignette.",
  "Encoding": "UTF-8",
  "License": "GPL-2",
  "URL": "https://github.com/reese3928/methylGSA",
  "BugReports": "https://github.com/reese3928/methylGSA/issues",
  "RoxygenNote": "6.1.0",
  "VignetteBuilder": "knitr",
  "biocViews": "DNAMethylation,DifferentialMethylation,GeneSetEnrichment,Regression,\nGeneRegulation,Pathways",
  "Config/pak/sysreqs": "libcairo2-dev cmake libfontconfig1-dev\nlibfreetype6-dev libglpk-dev make libbz2-dev libicu-dev\nliblzma-dev libpng-dev libuv1-dev libxml2-dev libssl-dev\nlibx11-dev xz-utils zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:48:17 UTC",
  "RemoteUrl": "https://github.com/bioc/methylGSA",
  "RemoteRef": "HEAD",
  "RemoteSha": "7792ec00a516cf0ab3462b5a88d6363a7f1e25ee",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-30 07:32:36 UTC",
    "User": "root"
  },
  "Author": "Xu Ren [aut, cre],\nPei Fen Kuan [aut]",
  "Maintainer": "Xu Ren <xuren2120@gmail.com>",
  "MD5sum": "e00b88c565b9508d0163efdaebd10c43",
  "_user": "bioc",
  "_type": "src",
  "_file": "methylGSA_1.31.0.tar.gz",
  "_fileid": "7211b91ca01a2fd53674654fcaaedb440790de8e5fcd6e46f2d5409885bc4dfe",
  "_filesize": 3227400,
  "_sha256": "7211b91ca01a2fd53674654fcaaedb440790de8e5fcd6e46f2d5409885bc4dfe",
  "_created": "2026-05-30T07:32:36.000Z",
  "_published": "2026-05-30T11:04:29.362Z",
  "_jobs": [
    {
      "job": 78633808874,
      "time": 1432,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7306646218"
    },
    {
      "job": 78633808881,
      "time": 1525,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7306655997"
    },
    {
      "job": 78633808888,
      "time": 1649,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7306668129"
    },
    {
      "job": 78633808876,
      "time": 1081,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7307718682"
    },
    {
      "job": 78633808891,
      "time": 839,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7307695629"
    },
    {
      "job": 78632601513,
      "time": 1327,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306501763"
    },
    {
      "job": 78633808933,
      "time": 1160,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306619332"
    },
    {
      "job": 78633808893,
      "time": 1322,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7306635103"
    },
    {
      "job": 78633808944,
      "time": 1230,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7306625981"
    },
    {
      "job": 78633808878,
      "time": 1408,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7306643782"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 11
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26677731353",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/methylGSA",
  "_commit": {
    "id": "7792ec00a516cf0ab3462b5a88d6363a7f1e25ee",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777380497
  },
  "_maintainer": {
    "name": "Xu Ren",
    "email": "xuren2120@gmail.com",
    "login": "reese3928",
    "description": "Staying at home.",
    "uuid": 13157014
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5",
      "role": "Depends"
    },
    {
      "package": "RobustRankAggreg",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "stringr",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "clusterProfiler",
      "role": "Imports"
    },
    {
      "package": "missMethyl",
      "role": "Imports"
    },
    {
      "package": "org.Hs.eg.db",
      "role": "Imports"
    },
    {
      "package": "reactome.db",
      "role": "Imports"
    },
    {
      "package": "BiocParallel",
      "role": "Imports"
    },
    {
      "package": "GO.db",
      "role": "Imports"
    },
    {
      "package": "AnnotationDbi",
      "role": "Imports"
    },
    {
      "package": "shiny",
      "role": "Imports"
    },
    {
      "package": "IlluminaHumanMethylation450kanno.ilmn12.hg19",
      "role": "Imports"
    },
    {
      "package": "IlluminaHumanMethylationEPICanno.ilm10b4.hg19",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "enrichplot",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.31.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.30.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "dnamethylation",
    "differentialmethylation",
    "genesetenrichment",
    "regression",
    "generegulation",
    "pathways",
    "enrichment",
    "generalized-linear-models",
    "logistic-regression",
    "methylation",
    "ontology",
    "shiny"
  ],
  "_stars": 13,
  "_contributors": [
    {
      "user": "reese3928",
      "count": 17,
      "uuid": 13157014
    },
    {
      "user": "nturaga",
      "count": 8,
      "uuid": 2746443
    },
    {
      "user": "vobencha",
      "count": 2,
      "uuid": 2466173
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 425,
    "source": "https://www.bioconductor.org/packages/stats/bioc/methylGSA"
  },
  "_mentions": 11,
  "_devurl": "https://github.com/reese3928/methylgsa",
  "_searchresults": 58,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/methylGSA.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/reese3928/methylgsa",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "barplot",
    "getDescription",
    "getGS",
    "methylglm",
    "methylgometh",
    "methylRRA",
    "prepareAnnot",
    "runExample"
  ],
  "_datasets": [
    {
      "name": "cpg.pval",
      "title": "An example of user input cpg.pval",
      "object": "cpgtoy",
      "file": "cpgtoy.RData",
      "class": [
        "numeric"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "CpG2Gene",
      "title": "An example of user user-supplied mapping between CpGs and genes",
      "object": "CpG2Genetoy",
      "file": "CpG2Genetoy.RData",
      "class": [
        "data.frame"
      ],
      "fields": [
        "CpG",
        "Gene"
      ],
      "rows": 364645,
      "table": true,
      "tojson": true
    },
    {
      "name": "GS.list",
      "title": "An example of user input gene sets",
      "object": "GSlisttoy",
      "file": "GSlisttoy.RData",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "barplot",
      "title": "Barplot for methylGSA analysis result",
      "topics": [
        "barplot"
      ]
    },
    {
      "page": "cpg.pval",
      "title": "An example of user input cpg.pval",
      "topics": [
        "cpg.pval"
      ]
    },
    {
      "page": "CpG2Gene",
      "title": "An example of user user-supplied mapping between CpGs and genes",
      "topics": [
        "CpG2Gene"
      ]
    },
    {
      "page": "getAnnot",
      "title": "Get CpG annotation",
      "topics": [
        "getAnnot"
      ]
    },
    {
      "page": "getDescription",
      "title": "Get gene set description",
      "topics": [
        "getDescription"
      ]
    },
    {
      "page": "getGS",
      "title": "Get Gene Sets",
      "topics": [
        "getGS"
      ]
    },
    {
      "page": "GS.list",
      "title": "An example of user input gene sets",
      "topics": [
        "GS.list"
      ]
    },
    {
      "page": "methylglm",
      "title": "Implement logistic regression adjusting for number of probes in enrichment analysis",
      "topics": [
        "methylglm"
      ]
    },
    {
      "page": "methylgometh",
      "title": "Adjusting number of probes in gene set testing using gometh or gsameth in missMethyl",
      "topics": [
        "methylgometh"
      ]
    },
    {
      "page": "methylRRA",
      "title": "Enrichment analysis after adjusting multiple p-values of each gene by Robust Rank Aggregation",
      "topics": [
        "methylRRA"
      ]
    },
    {
      "page": "prepareAnnot",
      "title": "Prepare user-supplied mapping between CpGs and genes.",
      "topics": [
        "prepareAnnot"
      ]
    },
    {
      "page": "runExample",
      "title": "methylGSA shiny app",
      "topics": [
        "runExample"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/methylGSA/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "aisdk",
    "annotate",
    "AnnotationDbi",
    "ape",
    "aplot",
    "askpass",
    "base64",
    "base64enc",
    "beanplot",
    "BH",
    "BiasedUrn",
    "Biobase",
    "BiocBaseUtils",
    "BiocGenerics",
    "BiocIO",
    "biocmake",
    "BiocParallel",
    "Biostrings",
    "bit",
    "bit64",
    "bitops",
    "blob",
    "bslib",
    "bumphunter",
    "cachem",
    "callr",
    "cigarillo",
    "cli",
    "clipr",
    "cluster",
    "clusterProfiler",
    "codetools",
    "commonmark",
    "cpp11",
    "crayon",
    "curl",
    "data.table",
    "DBI",
    "DelayedArray",
    "DelayedMatrixStats",
    "digest",
    "dir.expiry",
    "doRNG",
    "DOSE",
    "dplyr",
    "enrichit",
    "enrichplot",
    "evaluate",
    "farver",
    "fastmap",
    "FDb.InfiniumMethylation.hg19",
    "filelock",
    "fontawesome",
    "fontBitstreamVera",
    "fontLiberation",
    "fontquiver",
    "foreach",
    "formatR",
    "fs",
    "futile.logger",
    "futile.options",
    "gdtools",
    "genefilter",
    "generics",
    "GenomeInfoDb",
    "GenomicAlignments",
    "GenomicFeatures",
    "GenomicRanges",
    "GEOquery",
    "ggforce",
    "ggfun",
    "ggiraph",
    "ggnewscale",
    "ggplot2",
    "ggplotify",
    "ggrepel",
    "ggtangle",
    "ggtree",
    "glue",
    "GO.db",
    "GOSemSim",
    "gridExtra",
    "gridGraphics",
    "gson",
    "gtable",
    "h5mread",
    "HDF5Array",
    "highr",
    "hms",
    "htmltools",
    "htmlwidgets",
    "httpuv",
    "httr",
    "httr2",
    "igraph",
    "IlluminaHumanMethylation450kanno.ilmn12.hg19",
    "IlluminaHumanMethylation450kmanifest",
    "IlluminaHumanMethylationEPICanno.ilm10b4.hg19",
    "IlluminaHumanMethylationEPICmanifest",
    "IlluminaHumanMethylationEPICv2anno.20a1.hg38",
    "IlluminaHumanMethylationEPICv2manifest",
    "illuminaio",
    "IRanges",
    "isoband",
    "iterators",
    "jquerylib",
    "jsonlite",
    "KEGGREST",
    "knitr",
    "labeling",
    "lambda.r",
    "later",
    "lattice",
    "lazyeval",
    "lifecycle",
    "limma",
    "locfit",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "mclust",
    "memoise",
    "methylumi",
    "mime",
    "minfi",
    "missMethyl",
    "multtest",
    "nlme",
    "nor1mix",
    "openssl",
    "org.Hs.eg.db",
    "otel",
    "patchwork",
    "pillar",
    "pkgconfig",
    "plyr",
    "png",
    "polyclip",
    "preprocessCore",
    "prettyunits",
    "processx",
    "progress",
    "promises",
    "ps",
    "purrr",
    "quadprog",
    "qvalue",
    "R.methodsS3",
    "R.oo",
    "R.utils",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "RCurl",
    "reactome.db",
    "readr",
    "rentrez",
    "reshape",
    "reshape2",
    "restfulr",
    "rhdf5",
    "rhdf5filters",
    "Rhdf5lib",
    "Rhtslib",
    "rjson",
    "rlang",
    "rmarkdown",
    "rngtools",
    "RobustRankAggreg",
    "Rsamtools",
    "RSQLite",
    "rtracklayer",
    "ruv",
    "rvest",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "sass",
    "scales",
    "scatterpie",
    "scrime",
    "selectr",
    "Seqinfo",
    "shiny",
    "siggenes",
    "snow",
    "sourcetools",
    "SparseArray",
    "sparseMatrixStats",
    "statmod",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "survival",
    "sys",
    "systemfonts",
    "tibble",
    "tidydr",
    "tidyr",
    "tidyselect",
    "tidytree",
    "tinytex",
    "treeio",
    "tweenr",
    "TxDb.Hsapiens.UCSC.hg19.knownGene",
    "tzdb",
    "UCSC.utils",
    "utf8",
    "vctrs",
    "viridisLite",
    "vroom",
    "withr",
    "xfun",
    "XML",
    "xml2",
    "xtable",
    "XVector",
    "yaml",
    "yulab.utils"
  ],
  "_vignettes": [
    {
      "source": "methylGSA-vignette.Rmd",
      "filename": "methylGSA-vignette.html",
      "title": "methylGSA: Gene Set Analysis for DNA Methylation Datasets",
      "author": "Xu Ren and Pei Fen Kuan",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Installation",
        "Introduction",
        "Supported gene sets and gene ID types",
        "Supported array types",
        "Description of methylglm",
        "Example",
        "Description of methylRRA",
        "Description of methylgometh",
        "Other options",
        "Examples",
        "Visualization",
        "Session info",
        "References"
      ],
      "created": "2018-06-06 03:33:55",
      "modified": "2021-05-08 18:44:07",
      "commits": 14
    }
  ],
  "_score": 7.178401341533755,
  "_indexed": true,
  "_nocasepkg": "methylgsa",
  "_universes": [
    "bioc",
    "reese3928"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.31.0",
      "date": "2026-05-30T07:53:58.000Z",
      "distro": "noble",
      "commit": "7792ec00a516cf0ab3462b5a88d6363a7f1e25ee",
      "fileid": "5e3edfd4a5f09a20fa857495f71a33ebd101c0c5fc42165b453de1c93f909f53",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677731353"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.31.0",
      "date": "2026-05-30T07:56:05.000Z",
      "distro": "noble",
      "commit": "7792ec00a516cf0ab3462b5a88d6363a7f1e25ee",
      "fileid": "034bcdebfd320d4fe1825e573b890fc6447c14cda6f215369d0dbc8e9eb4f32c",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677731353"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.31.0",
      "date": "2026-05-30T11:00:14.000Z",
      "commit": "7792ec00a516cf0ab3462b5a88d6363a7f1e25ee",
      "fileid": "c2615dff3e30c9d60d61effc10c2d2c6bcea436768f651a53c7479be599b17ef",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677731353"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.31.0",
      "date": "2026-05-30T10:57:12.000Z",
      "commit": "7792ec00a516cf0ab3462b5a88d6363a7f1e25ee",
      "fileid": "d5c7d5c3b93a2eee087e6b7dd290c49f83af9de09093df640a1ef70636c193ec",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677731353"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.31.0",
      "date": "2026-05-30T07:52:43.000Z",
      "commit": "7792ec00a516cf0ab3462b5a88d6363a7f1e25ee",
      "fileid": "11928157ff5f95c900823888dc91af1048464956b1b46a19620c06ba63a60ea4",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677731353"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.31.0",
      "date": "2026-05-30T07:49:44.000Z",
      "commit": "7792ec00a516cf0ab3462b5a88d6363a7f1e25ee",
      "fileid": "1b0e350c0dd95815f72f87005e6450f4483c7eab12f65671f8f3b2d5914e2da3",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677731353"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.31.0",
      "date": "2026-05-30T07:48:00.000Z",
      "commit": "7792ec00a516cf0ab3462b5a88d6363a7f1e25ee",
      "fileid": "a2a569bcc421cb4a35734cecb0e9a0b40e087c4e9bb52d3edd58ed46bc208917",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677731353"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.31.0",
      "date": "2026-05-30T07:51:32.000Z",
      "commit": "7792ec00a516cf0ab3462b5a88d6363a7f1e25ee",
      "fileid": "a02c51690afd64210aee7fb89c311d7b5bf0e892822f52ad9eeedde4995b305f",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677731353"
    }
  ]
}