{
  "_id": "6ac28d74d743750d376d8c30",
  "Package": "CAGEWorkflow",
  "Type": "Package",
  "Title": "A step-by-step guide to analyzing CAGE data using R/Bioconductor",
  "Version": "1.28.0",
  "Authors@R": "person(\"Malte\", \"Thodberg\", email = \"maltethodberg@gmail.com\", role = c(\"aut\", \"cre\"))",
  "Description": "Workflow for analyzing Cap Analysis of Gene Expression\n(CAGE) data using R/Bioconductor.",
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "VignetteBuilder": "knitr",
  "Workflow": "true",
  "RoxygenNote": "7.1.2",
  "biocViews": "GeneExpressionWorkflow, AnnotationWorkflow",
  "Config/pak/sysreqs": "cmake libglpk-dev make libbz2-dev libicu-dev\nlibjpeg-dev liblzma-dev libpng-dev libuv1-dev libxml2-dev\nlibssl-dev xz-utils zlib1g-dev",
  "Repository": "Bioconductor 3.23",
  "Date/Publication": "2026-04-28 12:43:33 UTC",
  "RemoteUrl": "https://github.com/bioc/CAGEWorkflow",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "c85bab89862c4c931147f23db9a3e1839af02d61",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-04 17:21:07 UTC",
    "User": "root"
  },
  "Author": "Malte Thodberg [aut, cre]",
  "Maintainer": "Malte Thodberg <maltethodberg@gmail.com>",
  "_user": "bioc-release",
  "_type": "src",
  "_file": "CAGEWorkflow_1.28.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/f47365335d592ac975ac3e9143c86492415d67996838a47905ea69d2867e8f7b",
  "_filesize": 2681627,
  "_sha256": "f47365335d592ac975ac3e9143c86492415d67996838a47905ea69d2867e8f7b",
  "_expires": "2027-01-12T17:31:30.000Z",
  "_created": "2026-10-04T17:21:07.000Z",
  "_published": "2026-10-07T14:20:25.586Z",
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 9
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37219396894",
  "_status": "failure",
  "_upstream": "https://github.com/bioc/CAGEWorkflow",
  "_commit": {
    "id": "c85bab89862c4c931147f23db9a3e1839af02d61",
    "author": "lshep <lori.shepherd@roswellpark.org>",
    "committer": "lshep <lori.shepherd@roswellpark.org>",
    "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n",
    "time": 1777380213
  },
  "_maintainer": {
    "name": "Malte Thodberg",
    "email": "maltethodberg@gmail.com",
    "login": "maltethodberg",
    "description": "",
    "uuid": 10612774
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 111488865268,
      "time": 327,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11310347101"
    },
    {
      "job": 111488865317,
      "time": 569,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "11309679341"
    },
    {
      "job": 111488865294,
      "time": 418,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "11309663979"
    },
    {
      "job": 111488865285,
      "time": 224,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "11310277459"
    },
    {
      "job": 111488865333,
      "time": 229,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "11309228355"
    },
    {
      "job": 111486627577,
      "time": 685,
      "config": "source",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "11309693301"
    },
    {
      "job": 111488865320,
      "time": 314,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "11310400327"
    },
    {
      "job": 111488865299,
      "time": 218,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "11310068039"
    },
    {
      "job": 111488865321,
      "time": 280,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "11309868460"
    },
    {
      "job": 111488865322,
      "time": 278,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "11309238428"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.6.0",
      "role": "Depends"
    },
    {
      "package": "CAGEfightR",
      "role": "Depends"
    },
    {
      "package": "nanotubes",
      "role": "Depends"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "magick",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "BiocWorkflowTools",
      "role": "Suggests"
    },
    {
      "package": "pheatmap",
      "role": "Suggests"
    },
    {
      "package": "ggseqlogo",
      "role": "Suggests"
    },
    {
      "package": "viridis",
      "role": "Suggests"
    },
    {
      "package": "magrittr",
      "role": "Suggests"
    },
    {
      "package": "ggforce",
      "role": "Suggests"
    },
    {
      "package": "ggthemes",
      "role": "Suggests"
    },
    {
      "package": "tidyverse",
      "role": "Suggests"
    },
    {
      "package": "dplyr",
      "role": "Suggests"
    },
    {
      "package": "GenomicRanges",
      "role": "Suggests"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Suggests"
    },
    {
      "package": "GenomicFeatures",
      "role": "Suggests"
    },
    {
      "package": "BiocParallel",
      "role": "Suggests"
    },
    {
      "package": "InteractionSet",
      "role": "Suggests"
    },
    {
      "package": "Gviz",
      "role": "Suggests"
    },
    {
      "package": "DESeq2",
      "role": "Suggests"
    },
    {
      "package": "limma",
      "role": "Suggests"
    },
    {
      "package": "edgeR",
      "role": "Suggests"
    },
    {
      "package": "statmod",
      "role": "Suggests"
    },
    {
      "package": "BiasedUrn",
      "role": "Suggests"
    },
    {
      "package": "sva",
      "role": "Suggests"
    },
    {
      "package": "TFBSTools",
      "role": "Suggests"
    },
    {
      "package": "motifmatchr",
      "role": "Suggests"
    },
    {
      "package": "pathview",
      "role": "Suggests"
    },
    {
      "package": "BSgenome.Mmusculus.UCSC.mm9",
      "role": "Suggests"
    },
    {
      "package": "TxDb.Mmusculus.UCSC.mm9.knownGene",
      "role": "Suggests"
    },
    {
      "package": "org.Mm.eg.db",
      "role": "Suggests"
    },
    {
      "package": "JASPAR2016",
      "role": "Suggests"
    },
    {
      "package": "png",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_tags": [],
  "_topics": [
    "geneexpressionworkflow",
    "annotationworkflow"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 470,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/CAGEWorkflow.html",
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt"
  ],
  "_cranurl": false,
  "_exports": [],
  "_help": [],
  "_rundeps": [
    "abind",
    "AnnotationDbi",
    "AnnotationFilter",
    "askpass",
    "assertthat",
    "backports",
    "base64enc",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocFileCache",
    "BiocGenerics",
    "BiocIO",
    "BiocParallel",
    "biomaRt",
    "Biostrings",
    "biovizBase",
    "bit",
    "bit64",
    "bitops",
    "blob",
    "BSgenome",
    "bslib",
    "cachem",
    "CAGEfightR",
    "checkmate",
    "cigarillo",
    "cli",
    "cluster",
    "codetools",
    "colorspace",
    "cpp11",
    "crayon",
    "curl",
    "data.table",
    "DBI",
    "dbplyr",
    "DelayedArray",
    "deldir",
    "dichromat",
    "digest",
    "dplyr",
    "ensembldb",
    "evaluate",
    "farver",
    "fastmap",
    "filelock",
    "fontawesome",
    "foreign",
    "formatR",
    "Formula",
    "fs",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomeInfoDb",
    "GenomicAlignments",
    "GenomicFeatures",
    "GenomicFiles",
    "GenomicInteractions",
    "GenomicRanges",
    "ggplot2",
    "glue",
    "gridExtra",
    "gtable",
    "Gviz",
    "highr",
    "Hmisc",
    "hms",
    "htmlTable",
    "htmltools",
    "htmlwidgets",
    "httr",
    "httr2",
    "igraph",
    "InteractionSet",
    "interp",
    "IRanges",
    "isoband",
    "jpeg",
    "jquerylib",
    "jsonlite",
    "KEGGREST",
    "knitr",
    "labeling",
    "lambda.r",
    "lattice",
    "latticeExtra",
    "lazyeval",
    "lifecycle",
    "lobstr",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "mime",
    "nanotubes",
    "nnet",
    "openssl",
    "pillar",
    "pkgconfig",
    "png",
    "prettyunits",
    "progress",
    "ProtGenerics",
    "purrr",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "RcppEigen",
    "RCurl",
    "restfulr",
    "Rhtslib",
    "rjson",
    "rlang",
    "rmarkdown",
    "rpart",
    "Rsamtools",
    "RSQLite",
    "rstudioapi",
    "rtracklayer",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "sass",
    "scales",
    "Seqinfo",
    "snow",
    "SparseArray",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "tinytex",
    "UCSC.utils",
    "utf8",
    "VariantAnnotation",
    "vctrs",
    "viridisLite",
    "withr",
    "xfun",
    "XML",
    "xml2",
    "XVector",
    "yaml"
  ],
  "_score": 1.3010299956639813,
  "_indexed": false,
  "_nocasepkg": "cageworkflow",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://bioc.r-universe.dev/CAGEWorkflow",
  "_progress_url": "https://github.com/r-universe/bioc-release/actions/runs/37635809690",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.28.0",
      "date": "2026-10-04T17:29:55.000Z",
      "distro": "resolute",
      "commit": "c85bab89862c4c931147f23db9a3e1839af02d61",
      "fileid": "https://r2.ropensci.org/d8c9e36d278e2e99442c2a19bd0ff1353ce84f35a1d3152219439dd9935ffe35",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37219396894"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.28.0",
      "date": "2026-10-04T17:27:24.000Z",
      "distro": "resolute",
      "commit": "c85bab89862c4c931147f23db9a3e1839af02d61",
      "fileid": "https://r2.ropensci.org/ddb61034e52e23b1306d98fb1b708760dfe7af53f79c9c6dd3081ad0d1fce058",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37219396894"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.28.0",
      "date": "2026-10-04T17:24:26.000Z",
      "commit": "c85bab89862c4c931147f23db9a3e1839af02d61",
      "fileid": "https://r2.ropensci.org/b5a451bc406d4ebb08a9b217aaabac34beb792982512dbfe4166ac731bc6e3ef",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37219396894"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.28.0",
      "date": "2026-10-04T17:24:35.000Z",
      "commit": "c85bab89862c4c931147f23db9a3e1839af02d61",
      "fileid": "https://r2.ropensci.org/f5700ce1a74755afa1af9b2900f71a3d31503d8afbfc00a4f0a0003834ecbd16",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37219396894"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.28.0",
      "date": "2026-10-04T17:26:53.000Z",
      "commit": "c85bab89862c4c931147f23db9a3e1839af02d61",
      "fileid": "https://r2.ropensci.org/a79cbf94458edc08e9a4e3cb378ba26c2eb264d59a6e2c2f622fc5f667667efe",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37219396894"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.28.0",
      "date": "2026-10-04T17:24:13.000Z",
      "commit": "c85bab89862c4c931147f23db9a3e1839af02d61",
      "fileid": "https://r2.ropensci.org/bb8f4fdb2679957c374152a6064b63d69d4628bc8646a2748394557745a25570",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37219396894"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.28.0",
      "date": "2026-10-04T17:24:58.000Z",
      "commit": "c85bab89862c4c931147f23db9a3e1839af02d61",
      "fileid": "https://r2.ropensci.org/ced137f31afc12dae37a5843363bfec69be13638558336640c44b104c0af4bca",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37219396894"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.28.0",
      "date": "2026-10-04T17:25:00.000Z",
      "commit": "c85bab89862c4c931147f23db9a3e1839af02d61",
      "fileid": "https://r2.ropensci.org/9c2517e08d24bd3e291f7eef2ac823cc815cd28cc814a17486e3d130393fa8d2",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37219396894"
    }
  ]
}