{
  "_id": "6a202d1bcd65a98ecbd0bc78",
  "Package": "pairedGSEA",
  "Title": "Paired DGE and DGS analysis for gene set enrichment analysis",
  "Version": "1.13.0",
  "Authors@R": "c(\nperson(given = \"Dimitrios S.\",\nfamily = \"Kanakoglou\",\nemail = \"dimkan@dtu.dk\",\nrole = c(\"cre\", \"aut\")),\nperson(given = \"Søren Helweg\",\nfamily = \"Dam\",\nrole = c(\"aut\"),\ncomment = c(ORCID = \"0000-0002-9895-0930\")),\nperson(given = \"Lars Rønn\",\nfamily = \"Olsen\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0002-6725-7850\")),\nperson(given = \"Kristoffer\",\nfamily = \"Vitting-Seerup\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0002-6450-0608\"))\n)",
  "Description": "pairedGSEA makes it simple to run a paired Differential\nGene Expression (DGE) and Differencital Gene Splicing (DGS)\nanalysis. The package allows you to store intermediate results\nfor further investiation, if desired. pairedGSEA comes with a\nwrapper function for running an Over-Representation Analysis\n(ORA) and functionalities for plotting the results.",
  "License": "MIT + file LICENSE",
  "Config/testthat/edition": "3",
  "Encoding": "UTF-8",
  "Language": "en-US",
  "RoxygenNote": "7.3.3",
  "VignetteBuilder": "knitr",
  "biocViews": "DifferentialExpression, AlternativeSplicing,\nDifferentialSplicing, GeneExpression, ImmunoOncology,\nGeneSetEnrichment, Pathways, RNASeq, Software, Transcription,",
  "URL": "https://github.com/IsoformAnalysisGroup/pairedGSEA",
  "BugReports": "https://github.com/IsoformAnalysisGroup/pairedGSEA/issues",
  "Config/pak/sysreqs": "libfreetype6-dev libbz2-dev libicu-dev liblzma-dev\nlibpng-dev libxml2-dev libssl-dev xz-utils zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-05-13 10:53:08 UTC",
  "RemoteUrl": "https://github.com/bioc/pairedGSEA",
  "RemoteRef": "HEAD",
  "RemoteSha": "6ec0337063fb055421c4d53b381fa589dd286fcf",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-03 13:21:22 UTC",
    "User": "root"
  },
  "Author": "Dimitrios S. Kanakoglou [cre, aut],\nSøren Helweg Dam [aut] (ORCID: <https://orcid.org/0000-0002-9895-0930>),\nLars Rønn Olsen [aut] (ORCID: <https://orcid.org/0000-0002-6725-7850>),\nKristoffer Vitting-Seerup [aut] (ORCID:\n<https://orcid.org/0000-0002-6450-0608>)",
  "Maintainer": "Dimitrios S. Kanakoglou <dimkan@dtu.dk>",
  "MD5sum": "06dfcda67b7256a8043cd546b73a895b",
  "_user": "bioc",
  "_type": "src",
  "_file": "pairedGSEA_1.13.0.tar.gz",
  "_fileid": "61e8e4e9514d0f004ba422851b177dbc4ef2f6c5ffd251c34ded621686ece53e",
  "_filesize": 504928,
  "_sha256": "61e8e4e9514d0f004ba422851b177dbc4ef2f6c5ffd251c34ded621686ece53e",
  "_created": "2026-06-03T13:21:22.000Z",
  "_published": "2026-06-03T13:33:15.687Z",
  "_jobs": [
    {
      "job": 79304125798,
      "time": 208,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7385864162"
    },
    {
      "job": 79304125986,
      "time": 519,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7385985839"
    },
    {
      "job": 79304125715,
      "time": 501,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7385978870"
    },
    {
      "job": 79304125769,
      "time": 469,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7386032419"
    },
    {
      "job": 79304125790,
      "time": 517,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7386027022"
    },
    {
      "job": 79302938712,
      "time": 354,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7385777388"
    },
    {
      "job": 79304125757,
      "time": 168,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7385847641"
    },
    {
      "job": 79304125755,
      "time": 425,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7385949042"
    },
    {
      "job": 79304125834,
      "time": 464,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7385966387"
    },
    {
      "job": 79304125851,
      "time": 463,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7385963822"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 5
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26887246252",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/pairedGSEA",
  "_commit": {
    "id": "6ec0337063fb055421c4d53b381fa589dd286fcf",
    "author": "Søren Helweg Dam <49019552+shdam@users.noreply.github.com>",
    "committer": "GitHub <noreply@github.com>",
    "message": "Merge pull request #5 from IsoformAnalysisGroup/devel\n\nUpdate installation guide in README",
    "time": 1778669588
  },
  "_maintainer": {
    "name": "Dimitrios S. Kanakoglou",
    "email": "dimkan@dtu.dk",
    "login": "dskanakoglou",
    "description": "",
    "uuid": 131288809
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.4.0",
      "role": "Depends"
    },
    {
      "package": "DESeq2",
      "role": "Imports"
    },
    {
      "package": "DEXSeq",
      "role": "Imports"
    },
    {
      "package": "limma",
      "role": "Imports"
    },
    {
      "package": "fgsea",
      "role": "Imports"
    },
    {
      "package": "msigdbr",
      "role": "Imports"
    },
    {
      "package": "sva",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "BiocParallel",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "aggregation",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "showtext",
      "role": "Imports"
    },
    {
      "package": "writexl",
      "role": "Suggests"
    },
    {
      "package": "readxl",
      "role": "Suggests"
    },
    {
      "package": "readr",
      "role": "Suggests"
    },
    {
      "package": "rhdf5",
      "role": "Suggests"
    },
    {
      "package": "plotly",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "covr",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    },
    {
      "week": "2026-19",
      "n": 2
    },
    {
      "week": "2026-20",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.13.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.12.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "differentialexpression",
    "alternativesplicing",
    "differentialsplicing",
    "geneexpression",
    "immunooncology",
    "genesetenrichment",
    "pathways",
    "rnaseq",
    "software",
    "transcription"
  ],
  "_stars": 4,
  "_contributors": [
    {
      "user": "shdam",
      "count": 16,
      "uuid": 49019552
    },
    {
      "user": "jwokaty",
      "count": 14,
      "uuid": 1744257
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 244,
    "source": "https://www.bioconductor.org/packages/stats/bioc/pairedGSEA"
  },
  "_devurl": "https://github.com/isoformanalysisgroup/pairedgsea",
  "_searchresults": 4,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/pairedGSEA.html",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/isoformanalysisgroup/pairedgsea",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "paired_diff",
    "paired_ora",
    "plot_ora",
    "prepare_msigdb"
  ],
  "_datasets": [
    {
      "name": "example_diff_result",
      "title": "Output of running paired_diff on example_se.",
      "object": "example_diff_result",
      "file": "example_diff_result.rda",
      "class": [
        "DFrame"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "example_gene_sets",
      "title": "MSigDB gene sets from humans, category C5 with ensemble gene IDs",
      "object": "example_gene_sets",
      "file": "example_gene_sets.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "example_ora_results",
      "title": "Output of running paired_ora on example_diff_result and gene sets extracted from MSigDB",
      "object": "example_ora_results",
      "file": "example_ora_results.rda",
      "class": [
        "DFrame"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "example_se",
      "title": "A small subset of the GEO:GSE61220 data set.",
      "object": "example_se",
      "file": "example_se.rda",
      "class": [
        "SummarizedExperiment"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "example_diff_result",
      "title": "Output of running paired_diff on example_se.",
      "topics": [
        "example_diff_result"
      ]
    },
    {
      "page": "example_gene_sets",
      "title": "MSigDB gene sets from humans, category C5 with ensemble gene IDs",
      "topics": [
        "example_gene_sets"
      ]
    },
    {
      "page": "example_ora_results",
      "title": "Output of running paired_ora on example_diff_result and gene sets extracted from MSigDB",
      "topics": [
        "example_ora_results"
      ]
    },
    {
      "page": "example_se",
      "title": "A small subset of the GEO:GSE61220 data set.",
      "topics": [
        "example_se"
      ]
    },
    {
      "page": "paired_diff",
      "title": "Run paired DESeq2 and DEXSeq analyses",
      "concept": [
        "paired"
      ],
      "topics": [
        "paired_diff"
      ]
    },
    {
      "page": "paired_ora",
      "title": "Paired Over-Representation Analysis",
      "concept": [
        "paired"
      ],
      "topics": [
        "paired_ora"
      ]
    },
    {
      "page": "plot_ora",
      "title": "Scatter plot of Over-Representation Analysis results",
      "concept": [
        "plotting"
      ],
      "topics": [
        "plot_ora"
      ]
    },
    {
      "page": "prepare_msigdb",
      "title": "Load MSigDB and convert to names list of gene sets",
      "topics": [
        "prepare_msigdb"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/pairedGSEA/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "aggregation",
    "annotate",
    "AnnotationDbi",
    "askpass",
    "assertthat",
    "babelgene",
    "BH",
    "Biobase",
    "BiocFileCache",
    "BiocGenerics",
    "BiocParallel",
    "biomaRt",
    "Biostrings",
    "bit",
    "bit64",
    "bitops",
    "blob",
    "cachem",
    "cli",
    "codetools",
    "cowplot",
    "cpp11",
    "crayon",
    "curl",
    "data.table",
    "DBI",
    "dbplyr",
    "DelayedArray",
    "DESeq2",
    "DEXSeq",
    "dplyr",
    "edgeR",
    "farver",
    "fastmap",
    "fastmatch",
    "fgsea",
    "filelock",
    "formatR",
    "futile.logger",
    "futile.options",
    "genefilter",
    "geneplotter",
    "generics",
    "GenomicRanges",
    "ggplot2",
    "glue",
    "gtable",
    "hms",
    "httr",
    "httr2",
    "hwriter",
    "IRanges",
    "isoband",
    "jsonlite",
    "KEGGREST",
    "labeling",
    "lambda.r",
    "lattice",
    "lifecycle",
    "limma",
    "locfit",
    "magrittr",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "mgcv",
    "mime",
    "msigdbr",
    "nlme",
    "openssl",
    "pillar",
    "pkgconfig",
    "png",
    "prettyunits",
    "progress",
    "purrr",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "Rhtslib",
    "rlang",
    "Rsamtools",
    "RSQLite",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "scales",
    "Seqinfo",
    "showtext",
    "showtextdb",
    "snow",
    "SparseArray",
    "statmod",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "survival",
    "sva",
    "sys",
    "sysfonts",
    "tibble",
    "tidyr",
    "tidyselect",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr",
    "XML",
    "xml2",
    "xtable",
    "XVector"
  ],
  "_vignettes": [
    {
      "source": "User-Guide.Rmd",
      "filename": "User-Guide.html",
      "title": "User Guide",
      "author": "Søren Helweg Dam",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Installation",
        "Interoperability with IsoformSwitchAnalyzeR",
        "Paired differential expression and splicing",
        "Preparing the experiment parameters",
        "Check your metadata",
        "Running the analysis",
        "Additional parameters",
        "Over-Representation Analysis",
        "Running the inbuilt ORA function",
        "Analysing ORA results",
        "Scatter plot of enrichment scores",
        "Session Info",
        "References"
      ],
      "created": "2022-08-09 13:33:40",
      "modified": "2026-05-05 09:27:12",
      "commits": 17
    }
  ],
  "_score": 4.903089986991944,
  "_indexed": true,
  "_nocasepkg": "pairedgsea",
  "_universes": [
    "bioc",
    "dskanakoglou",
    "isoformanalysisgroup"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.13.0",
      "date": "2026-06-03T13:24:58.000Z",
      "distro": "noble",
      "commit": "6ec0337063fb055421c4d53b381fa589dd286fcf",
      "fileid": "4f817f10ea8ae8234b761e96ebfe342dc19268437e1ea6b01c6b51894500490f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26887246252"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.13.0",
      "date": "2026-06-03T13:25:13.000Z",
      "distro": "noble",
      "commit": "6ec0337063fb055421c4d53b381fa589dd286fcf",
      "fileid": "09de9ed47fd76b6052d630e0a2fc4815a973afeb2f4261d9f75683f497faa138",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26887246252"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.13.0",
      "date": "2026-06-03T13:26:54.000Z",
      "commit": "6ec0337063fb055421c4d53b381fa589dd286fcf",
      "fileid": "8659dc99691d779896f1d1f7aa6fe381a7e410169d645d507f2574d88c81e0ef",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26887246252"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.13.0",
      "date": "2026-06-03T13:26:06.000Z",
      "commit": "6ec0337063fb055421c4d53b381fa589dd286fcf",
      "fileid": "e880db252f6493f309f4067ce7eda738654abb074d93c7e034e154baa04c6252",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26887246252"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.13.0",
      "date": "2026-06-03T13:24:51.000Z",
      "commit": "6ec0337063fb055421c4d53b381fa589dd286fcf",
      "fileid": "be00778f6912c458560109f788fe6bb8a4f4c41e9c4c2d17dbef741e74134b34",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26887246252"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.13.0",
      "date": "2026-06-03T13:23:44.000Z",
      "commit": "6ec0337063fb055421c4d53b381fa589dd286fcf",
      "fileid": "feb52cd4198feb4bf731ae72096fe485b859ae47fc99d19d71a910b465ad5cd5",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26887246252"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.13.0",
      "date": "2026-06-03T13:24:04.000Z",
      "commit": "6ec0337063fb055421c4d53b381fa589dd286fcf",
      "fileid": "cbc6aac4216f23d0886aef91c52a242914b497da6bab562a0d89961493cffcbb",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26887246252"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.13.0",
      "date": "2026-06-03T13:23:50.000Z",
      "commit": "6ec0337063fb055421c4d53b381fa589dd286fcf",
      "fileid": "12ddc8f328dc46788bdf734d0df11194169d68af1fcddb2285b3c435ae783666",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26887246252"
    }
  ]
}