{ "_id": "6a30f6883efcd9bda434cad3", "Package": "Glimma", "Type": "Package", "Title": "Interactive visualizations for gene expression analysis", "Version": "2.22.1", "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-release.r-universe.dev", "Date/Publication": "2026-06-16 01:02:14 UTC", "RemoteUrl": "https://github.com/bioc/Glimma", "RemoteRef": "RELEASE_3_23", "RemoteSha": "175f4cddf7aec00054f9519daaf6e6bd1e3f4a03", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-16 06:41:15 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 ", "MD5sum": "322008808d02555a472eda47c2ff8c0f", "_user": "bioc-release", "_type": "src", "_file": "Glimma_2.22.1.tar.gz", "_fileid": "eda4d487e319c818cdc333318c83638690889f38671e731bb9f256729952347d", "_filesize": 5029439, "_sha256": "eda4d487e319c818cdc333318c83638690889f38671e731bb9f256729952347d", "_created": "2026-06-16T06:41:15.000Z", "_published": "2026-06-16T07:08:56.437Z", "_jobs": [ { "job": 81596481100, "time": 270, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7659312300" }, { "job": 81596481092, "time": 404, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7659349881" }, { "job": 81596481099, "time": 477, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7659371112" }, { "job": 81596481104, "time": 250, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7659337061" }, { "job": 81596481081, "time": 250, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7659321413" }, { "job": 81594908087, "time": 697, "config": "source", "r": "4.6.0", "check": "ERROR", "artifact": "7659238134" }, { "job": 81596481113, "time": 222, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7659300672" }, { "job": 81596481136, "time": 1498, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "7659670880" }, { "job": 81596481130, "time": 1452, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7659658125" }, { "job": 81596481115, "time": 1339, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7659624760" } ], "_bioccheck": { "error": 1, "warning": 0, "note": 15 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27598826367", "_status": "failure", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/Glimma", "_commit": { "id": "175f4cddf7aec00054f9519daaf6e6bd1e3f4a03", "author": "shians ", "committer": "shians ", "message": "Version match to release\n", "time": 1781571734 }, "_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": false, "_usedby": 2, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 4 }, { "week": "2026-25", "n": 1 } ], "_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", "followers": 440, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_mentions": 17, "_devurl": "https://github.com/hasaru-k/glimmav2", "_searchresults": 848, "_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", "LICENSE", "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/RELEASE_3_23/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" ], "_score": 9.125676410382333, "_indexed": false, "_nocasepkg": "glimma", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/Glimma", "_previous": "2.22.0", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.22.1", "date": "2026-06-16T06:47:07.000Z", "distro": "noble", "commit": "175f4cddf7aec00054f9519daaf6e6bd1e3f4a03", "fileid": "ad750c5a826fbcef5143dccd317cef80ef7083d81f1494a1d30a178742ca364b", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27598826367" }, { "r": "4.6.0", "os": "linux", "version": "2.22.1", "date": "2026-06-16T06:48:09.000Z", "distro": "noble", "commit": "175f4cddf7aec00054f9519daaf6e6bd1e3f4a03", "fileid": "4b7cb5854418e9ec15418fe10ddb84439c5cc9badb0c0d9b9e44df7e02eb51f5", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27598826367" }, { "r": "4.5.3", "os": "mac", "version": "2.22.1", "date": "2026-06-16T06:47:15.000Z", "commit": "175f4cddf7aec00054f9519daaf6e6bd1e3f4a03", "fileid": "8227f35e70273720122eb43a1d07fd217ad406bdee32d9b0cbdd8450f13fbeac", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27598826367" }, { "r": "4.6.0", "os": "mac", "version": "2.22.1", "date": "2026-06-16T06:46:16.000Z", "commit": "175f4cddf7aec00054f9519daaf6e6bd1e3f4a03", "fileid": "f7ca49aa0a5a02aacccbd764151a1103eaff1bd9b6655f0e6d3da10dc3cce9cc", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27598826367" }, { "r": "4.6.0", "os": "wasm", "version": "2.22.1", "date": "2026-06-16T06:47:16.000Z", "commit": "175f4cddf7aec00054f9519daaf6e6bd1e3f4a03", "fileid": "cef0313752c17e79215e331740cf2cbb1d75ef25f81a2a1461f283b70f5717e2", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27598826367" }, { "r": "4.7.0", "os": "win", "version": "2.22.1", "date": "2026-06-16T07:03:52.000Z", "commit": "175f4cddf7aec00054f9519daaf6e6bd1e3f4a03", "fileid": "d43ce15c462f8353ca6e3904d63b58ef420e9369783a54529e8ec021c35def22", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27598826367" }, { "r": "4.5.3", "os": "win", "version": "2.22.1", "date": "2026-06-16T07:03:23.000Z", "commit": "175f4cddf7aec00054f9519daaf6e6bd1e3f4a03", "fileid": "4f13d1a50f7351cb7a79861c6cae6f9c231b861e247b6a9a9bead51e410e58a3", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27598826367" }, { "r": "4.6.0", "os": "win", "version": "2.22.1", "date": "2026-06-16T07:01:28.000Z", "commit": "175f4cddf7aec00054f9519daaf6e6bd1e3f4a03", "fileid": "580facff0da0cba49eda18166ff0e9a427ee9762daea51de3a93ea7ab76cd28c", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27598826367" } ] }