{
  "_id": "6a1af7951d7bb097a09fa76a",
  "Package": "Glimma",
  "Type": "Package",
  "Title": "Interactive visualizations for gene expression analysis",
  "Version": "2.23.1",
  "Authors@R": "c(\nperson(\n\"Shian\", \"Su\",\nrole = c(\"aut\", \"cre\"),\nemail = \"su.s@wehi.edu.au\"\n),\nperson(\n\"Hasaru\", \"Kariyawasam\",\nrole = c(\"aut\")\n),\nperson(\n\"Oliver\", \"Voogd\",\nrole = c(\"aut\")\n),\nperson(\n\"Matthew\", \"Ritchie\",\nrole = c(\"aut\")\n),\nperson(\n\"Charity\", \"Law\",\nrole = c(\"aut\")\n),\nperson(\n\"Stuart\", \"Lee\",\nrole = c(\"ctb\")\n),\nperson(\n\"Isaac\", \"Virshup\",\nrole = c(\"ctb\")\n)\n)",
  "Description": "This package produces interactive visualizations for\nRNA-seq data analysis, utilizing output from limma, edgeR, or\nDESeq2. It produces interactive htmlwidgets versions of popular\nRNA-seq analysis plots to enhance the exploration of analysis\nresults by overlaying interactive features. The plots can be\nviewed in a web browser or embedded in notebook documents.",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.3.2",
  "biocViews": "DifferentialExpression, GeneExpression, Microarray,\nReportWriting, RNASeq, Sequencing, Visualization",
  "License": "GPL-3",
  "URL": "https://github.com/hasaru-k/GlimmaV2",
  "BugReports": "https://github.com/hasaru-k/GlimmaV2/issues",
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "cmake make libuv1-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-30 14:24:55 UTC",
  "RemoteUrl": "https://github.com/bioc/Glimma",
  "RemoteRef": "HEAD",
  "RemoteSha": "59966a16c6211356e01a4dc87a1add3574f2e810",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-30 09:47:09 UTC",
    "User": "root"
  },
  "Author": "Shian Su [aut, cre],\nHasaru Kariyawasam [aut],\nOliver Voogd [aut],\nMatthew Ritchie [aut],\nCharity Law [aut],\nStuart Lee [ctb],\nIsaac Virshup [ctb]",
  "Maintainer": "Shian Su <su.s@wehi.edu.au>",
  "MD5sum": "3e0ebfcd9369682572c9cc5b916c6045",
  "_user": "bioc",
  "_type": "src",
  "_file": "Glimma_2.23.1.tar.gz",
  "_fileid": "3d830048d12447912d0a0143e6f5aca68a20982ece29a164064c72c9e248ad4e",
  "_filesize": 11020775,
  "_sha256": "3d830048d12447912d0a0143e6f5aca68a20982ece29a164064c72c9e248ad4e",
  "_created": "2026-05-30T09:47:09.000Z",
  "_published": "2026-05-30T14:43:33.539Z",
  "_jobs": [
    {
      "job": 78640653620,
      "time": 234,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7307501010"
    },
    {
      "job": 78640653643,
      "time": 496,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7307522708"
    },
    {
      "job": 78640653640,
      "time": 511,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7307523357"
    },
    {
      "job": 78640653631,
      "time": 349,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7308962204"
    },
    {
      "job": 78640653626,
      "time": 292,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7308955540"
    },
    {
      "job": 78639692575,
      "time": 630,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307294113"
    },
    {
      "job": 78640653621,
      "time": 209,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307498836"
    },
    {
      "job": 78640653619,
      "time": 1519,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7307619749"
    },
    {
      "job": 78640653625,
      "time": 1492,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7307617282"
    },
    {
      "job": 78640653624,
      "time": 1410,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7307609027"
    }
  ],
  "_bioccheck": {
    "error": 1,
    "warning": 0,
    "note": 15
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26676325786",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/Glimma",
  "_commit": {
    "id": "59966a16c6211356e01a4dc87a1add3574f2e810",
    "author": "hasaru-k <35970468+hasaru-k@users.noreply.github.com>",
    "committer": "hasaru-k <35970468+hasaru-k@users.noreply.github.com>",
    "message": ".\n",
    "time": 1777559095
  },
  "_maintainer": {
    "name": "Shian Su",
    "email": "su.s@wehi.edu.au",
    "login": "shians",
    "description": "Bioinformatician with an interest in high-throughput genomics and epigenomics. Experienced in R and C++.",
    "uuid": 6036662
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.0.0",
      "role": "Depends"
    },
    {
      "package": "htmlwidgets",
      "role": "Imports"
    },
    {
      "package": "edgeR",
      "role": "Imports"
    },
    {
      "package": "DESeq2",
      "role": "Imports"
    },
    {
      "package": "limma",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "jsonlite",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "IRanges",
      "role": "Suggests"
    },
    {
      "package": "GenomicRanges",
      "role": "Suggests"
    },
    {
      "package": "purrr",
      "role": "Suggests"
    },
    {
      "package": "AnnotationHub",
      "role": "Suggests"
    },
    {
      "package": "scRNAseq",
      "role": "Suggests"
    },
    {
      "package": "scater",
      "role": "Suggests"
    },
    {
      "package": "scran",
      "role": "Suggests"
    },
    {
      "package": "scRNAseq",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 2,
  "_updates": [
    {
      "week": "2025-24",
      "n": 2
    },
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 4
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "2.23.1",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "2.21.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "differentialexpression",
    "geneexpression",
    "microarray",
    "reportwriting",
    "rnaseq",
    "sequencing",
    "visualization",
    "differential-expression",
    "interactive-visualizations"
  ],
  "_stars": 35,
  "_contributors": [
    {
      "user": "hasaru-k",
      "count": 180,
      "uuid": 35970468
    },
    {
      "user": "shians",
      "count": 118,
      "uuid": 6036662
    },
    {
      "user": "olivervoogd",
      "count": 27,
      "uuid": 51314988
    },
    {
      "user": "charitylaw",
      "count": 11,
      "uuid": 8265780
    },
    {
      "user": "mikelove",
      "count": 1,
      "uuid": 69203
    },
    {
      "user": "nghiaagent",
      "count": 1,
      "uuid": 8216540
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 1814,
    "source": "https://www.bioconductor.org/packages/stats/bioc/Glimma"
  },
  "_mentions": 17,
  "_devurl": "https://github.com/hasaru-k/glimmav2",
  "_searchresults": 748,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/Glimma.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/mritchielab/glimmav2",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "glimmaMA",
    "glimmaMD",
    "glimmaMDS",
    "glimmaVolcano",
    "glimmaXY",
    "glMDPlot",
    "glMDRmd",
    "glMDSPlot",
    "glXYPlot"
  ],
  "_help": [
    {
      "page": "as.hexcol",
      "title": "Numeric to hex colour converter",
      "topics": [
        "as.hexcol"
      ]
    },
    {
      "page": "glimma",
      "title": "Glimma: interactive graphics from limma",
      "topics": [
        "Glimma-package",
        "Glimma",
        "glimma"
      ]
    },
    {
      "page": "glimmaMA",
      "title": "Glimma MA Plot",
      "topics": [
        "glimmaMA",
        "glimmaMD"
      ]
    },
    {
      "page": "glimmaMA.DESeqDataSet",
      "title": "Glimma MA Plot",
      "topics": [
        "glimmaMA.DESeqDataSet"
      ]
    },
    {
      "page": "glimmaMA.DGEExact",
      "title": "Glimma MA Plot",
      "topics": [
        "glimmaMA.DGEExact"
      ]
    },
    {
      "page": "glimmaMA.DGELRT",
      "title": "Glimma MA Plot",
      "topics": [
        "glimmaMA.DGELRT"
      ]
    },
    {
      "page": "glimmaMA.MArrayLM",
      "title": "Glimma MA Plot",
      "topics": [
        "glimmaMA.MArrayLM"
      ]
    },
    {
      "page": "glimmaMDS",
      "title": "Glimma MDS Plot",
      "topics": [
        "glimmaMDS"
      ]
    },
    {
      "page": "glimmaMDS.default",
      "title": "Glimma MDS Plot",
      "topics": [
        "glimmaMDS.default"
      ]
    },
    {
      "page": "glimmaMDS.DESeqDataSet",
      "title": "Glimma MDS Plot",
      "topics": [
        "glimmaMDS.DESeqDataSet"
      ]
    },
    {
      "page": "glimmaMDS.DGEList",
      "title": "Glimma MDS Plot",
      "topics": [
        "glimmaMDS.DGEList"
      ]
    },
    {
      "page": "glimmaVolcano",
      "title": "Glimma Volcano Plot",
      "topics": [
        "glimmaVolcano"
      ]
    },
    {
      "page": "glimmaVolcano.DESeqDataSet",
      "title": "Glimma Volcano Plot",
      "topics": [
        "glimmaVolcano.DESeqDataSet"
      ]
    },
    {
      "page": "glimmaVolcano.DGEExact",
      "title": "Glimma Volcano Plot",
      "topics": [
        "glimmaVolcano.DGEExact"
      ]
    },
    {
      "page": "glimmaVolcano.DGELRT",
      "title": "Glimma Volcano Plot",
      "topics": [
        "glimmaVolcano.DGELRT"
      ]
    },
    {
      "page": "glimmaVolcano.MArrayLM",
      "title": "Glimma Volcano Plot",
      "topics": [
        "glimmaVolcano.MArrayLM"
      ]
    },
    {
      "page": "glimmaXY",
      "title": "Glimma XY Plot",
      "topics": [
        "glimmaXY"
      ]
    },
    {
      "page": "glMDPlot",
      "title": "Glimma MD Plot",
      "topics": [
        "glMDPlot"
      ]
    },
    {
      "page": "glMDPlot.default",
      "title": "Glimma MD Plot",
      "topics": [
        "glMDPlot.default"
      ]
    },
    {
      "page": "glMDPlot.DESeqDataSet",
      "title": "Glimma MD Plot",
      "topics": [
        "glMDPlot.DESeqDataSet"
      ]
    },
    {
      "page": "glMDPlot.DESeqResults",
      "title": "Glimma MD Plot",
      "topics": [
        "glMDPlot.DESeqResults"
      ]
    },
    {
      "page": "glMDPlot.DGEExact",
      "title": "Glimma MD Plot",
      "topics": [
        "glMDPlot.DGEExact"
      ]
    },
    {
      "page": "glMDPlot.DGELRT",
      "title": "Glimma MD Plot",
      "topics": [
        "glMDPlot.DGELRT"
      ]
    },
    {
      "page": "glMDPlot.MArrayLM",
      "title": "Glimma MD Plot",
      "topics": [
        "glMDPlot.MArrayLM"
      ]
    },
    {
      "page": "glMDRmd",
      "title": "glMDPlot Rmarkdown link and instructions",
      "topics": [
        "glMDRmd"
      ]
    },
    {
      "page": "glMDSPlot",
      "title": "Glimma MDS Plot",
      "topics": [
        "glMDSPlot"
      ]
    },
    {
      "page": "glMDSPlot.default",
      "title": "Glimma MDS Plot",
      "topics": [
        "glMDSPlot.default"
      ]
    },
    {
      "page": "glMDSPlot.DESeqDataSet",
      "title": "Glimma MDS Plot",
      "topics": [
        "glMDSPlot.DESeqDataSet"
      ]
    },
    {
      "page": "glMDSPlot.DGEList",
      "title": "Glimma MDS Plot",
      "topics": [
        "glMDSPlot.DGEList"
      ]
    },
    {
      "page": "glXYPlot",
      "title": "Glimma XY Plot",
      "topics": [
        "glXYPlot"
      ]
    },
    {
      "page": "is.hex",
      "title": "Hexcode colours",
      "topics": [
        "is.hex"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/Glimma/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "base64enc",
    "BH",
    "Biobase",
    "BiocGenerics",
    "BiocParallel",
    "bslib",
    "cachem",
    "cli",
    "codetools",
    "cpp11",
    "DelayedArray",
    "DESeq2",
    "digest",
    "edgeR",
    "evaluate",
    "farver",
    "fastmap",
    "fontawesome",
    "formatR",
    "fs",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicRanges",
    "ggplot2",
    "glue",
    "gtable",
    "highr",
    "htmltools",
    "htmlwidgets",
    "IRanges",
    "isoband",
    "jquerylib",
    "jsonlite",
    "knitr",
    "labeling",
    "lambda.r",
    "lattice",
    "lifecycle",
    "limma",
    "locfit",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "mime",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "rlang",
    "rmarkdown",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "sass",
    "scales",
    "Seqinfo",
    "snow",
    "SparseArray",
    "statmod",
    "SummarizedExperiment",
    "tinytex",
    "vctrs",
    "viridisLite",
    "withr",
    "xfun",
    "XVector",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "DESeq2.Rmd",
      "filename": "DESeq2.html",
      "title": "DESeq2",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "MDS Plot",
        "Interactions with the plot",
        "Modifications to the plot",
        "MA Plot",
        "Saving widgets",
        "Session Info"
      ],
      "created": "2020-10-21 10:41:43",
      "modified": "2021-09-23 13:23:21",
      "commits": 4
    },
    {
      "source": "limma_edger.Rmd",
      "filename": "limma_edger.html",
      "title": "Introduction using limma or edgeR",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "MDS Plot",
        "Interactions with the plot",
        "Modifications to the plot",
        "MA Plot",
        "Using limma",
        "Using edgeR",
        "Volcano Plot",
        "Saving widgets",
        "Session Info"
      ],
      "created": "2020-10-21 10:41:43",
      "modified": "2022-03-08 04:50:18",
      "commits": 5
    },
    {
      "source": "single_cell_edger.Rmd",
      "filename": "single_cell_edger.html",
      "title": "Single Cells with edgeR",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Session Info"
      ],
      "created": "2021-09-20 06:29:24",
      "modified": "2022-03-08 04:50:18",
      "commits": 2
    }
  ],
  "_score": 10.80694069343382,
  "_indexed": true,
  "_nocasepkg": "glimma",
  "_universes": [
    "bioc",
    "shians",
    "hasaru-k"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.23.1",
      "date": "2026-05-30T10:26:13.000Z",
      "distro": "noble",
      "commit": "59966a16c6211356e01a4dc87a1add3574f2e810",
      "fileid": "28bfb5a3a6400cf53b759f4a0572185d7ee33e85f720e7f91c8c4ee2b89e357a",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676325786"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "2.23.1",
      "date": "2026-05-30T10:26:25.000Z",
      "distro": "noble",
      "commit": "59966a16c6211356e01a4dc87a1add3574f2e810",
      "fileid": "20794bb6ae662fa2c444905cd4a0be605efab6b866ebe9cd06e489399f4e961c",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676325786"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.23.1",
      "date": "2026-05-30T14:39:24.000Z",
      "commit": "59966a16c6211356e01a4dc87a1add3574f2e810",
      "fileid": "e61394414cc252ec9a0698c6d2d108dc790dedf2903f28dab6472d428b712012",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676325786"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "2.23.1",
      "date": "2026-05-30T14:39:03.000Z",
      "commit": "59966a16c6211356e01a4dc87a1add3574f2e810",
      "fileid": "247258bf2a25b34824a6c09058bd88a012be1a84031ae1ac4acb53a11589cd82",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676325786"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "2.23.1",
      "date": "2026-05-30T10:25:10.000Z",
      "commit": "59966a16c6211356e01a4dc87a1add3574f2e810",
      "fileid": "08c68ca08824e3b5988e9cde0e462a71bbe10e393b7c8409699fba38c6e3c75c",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676325786"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "2.23.1",
      "date": "2026-05-30T10:42:15.000Z",
      "commit": "59966a16c6211356e01a4dc87a1add3574f2e810",
      "fileid": "1815709d0d1e9a77f86d8b0bf2ec8345b03e94bf542c95573bfa181853b2431c",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676325786"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "2.23.1",
      "date": "2026-05-30T10:41:57.000Z",
      "commit": "59966a16c6211356e01a4dc87a1add3574f2e810",
      "fileid": "49d78448f4e4e729bcb775b4a4575fc4d39b897829b12cada5e385c121d929fa",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676325786"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "2.23.1",
      "date": "2026-05-30T10:40:58.000Z",
      "commit": "59966a16c6211356e01a4dc87a1add3574f2e810",
      "fileid": "4213e5da33f4f73106b5747dd4f885f49d245cf76f5f01edf75fdb549ae12ed1",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676325786"
    }
  ]
}