{
  "_id": "6a21285fcd65a98ecbd21c16",
  "Package": "gDNAx",
  "Type": "Package",
  "Title": "Diagnostics for assessing genomic DNA contamination in RNA-seq\ndata",
  "Version": "1.10.0",
  "Authors@R": "c(\nperson(\"Beatriz\", \"Calvo-Serra\", email = \"beatriz.calvo@upf.edu\", role = c(\"aut\")),\nperson(\"Robert\", \"Castelo\", email = \"robert.castelo@upf.edu\", role = c(\"aut\", \"cre\")))",
  "Description": "Provides diagnostics for assessing genomic DNA\ncontamination in RNA-seq data, as well as plots representing\nthese diagnostics. Moreover, the package can be used to get an\ninsight into the strand library protocol used and, in case of\nstrand-specific libraries, the strandedness of the data.\nFurthermore, it provides functionality to filter out reads of\npotential gDNA origin.",
  "License": "Artistic-2.0",
  "Encoding": "UTF-8",
  "biocViews": "Transcription, Transcriptomics, RNASeq, Sequencing,\nPreprocessing, Software, GeneExpression, Coverage,\nDifferentialExpression, FunctionalGenomics, SplicedAlignment,\nAlignment",
  "VignetteBuilder": "knitr",
  "Roxygen": "list(markdown=TRUE)",
  "RoxygenNote": "7.3.3",
  "URL": "https://github.com/functionalgenomics/gDNAx",
  "BugReports": "https://github.com/functionalgenomics/gDNAx/issues",
  "Collate": "'AllGenerics.R' 'AllClasses.R' 'utils.R' 'dx.R'\n'filterBAMtx.R' 'tx.R' 'strandedness.R' 'gDNAx.R'\n'gDNAx-pkg-deprecated.R'",
  "Config/pak/sysreqs": "make libbz2-dev libicu-dev liblzma-dev libpng-dev\nlibxml2-dev libssl-dev xz-utils zlib1g-dev",
  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 13:01:25 UTC",
  "RemoteUrl": "https://github.com/bioc/gDNAx",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "fccf1b0ad2c1cbed6df21b2d1206092f155bccdb",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-04 07:12:40 UTC",
    "User": "root"
  },
  "Author": "Beatriz Calvo-Serra [aut],\nRobert Castelo [aut, cre]",
  "Maintainer": "Robert Castelo <robert.castelo@upf.edu>",
  "MD5sum": "8838f74b4fc6f4ffd23a42e3b7420a20",
  "_user": "bioc-release",
  "_type": "src",
  "_file": "gDNAx_1.10.0.tar.gz",
  "_fileid": "147b7b1205d5301cd862187b017125f890f3c9fc9313927d09fe59471899d748",
  "_filesize": 621548,
  "_sha256": "147b7b1205d5301cd862187b017125f890f3c9fc9313927d09fe59471899d748",
  "_created": "2026-06-04T07:12:40.000Z",
  "_published": "2026-06-04T07:25:19.290Z",
  "_jobs": [
    {
      "job": 79468440377,
      "time": 240,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7405313292"
    },
    {
      "job": 79468440430,
      "time": 593,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "7405408873"
    },
    {
      "job": 79468440366,
      "time": 573,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7405403224"
    },
    {
      "job": 79468440339,
      "time": 541,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7405412346"
    },
    {
      "job": 79468440350,
      "time": 633,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7405432443"
    },
    {
      "job": 79467435899,
      "time": 440,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7405246162"
    },
    {
      "job": 79468440392,
      "time": 189,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7405299599"
    },
    {
      "job": 79468440389,
      "time": 523,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7405388900"
    },
    {
      "job": 79468440337,
      "time": 642,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7405421695"
    },
    {
      "job": 79468440353,
      "time": 674,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7405431030"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 1,
    "note": 11
  },
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26936490411",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/gDNAx",
  "_commit": {
    "id": "fccf1b0ad2c1cbed6df21b2d1206092f155bccdb",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n",
    "time": 1777381285
  },
  "_maintainer": {
    "name": "Robert Castelo",
    "email": "robert.castelo@upf.edu",
    "login": "rcastelo",
    "twitter": "@robertclab",
    "description": "biostatistics, machine learning, genetics, genomics, R/Bioconductor",
    "uuid": 1677433
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.3",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "BiocGenerics",
      "role": "Imports"
    },
    {
      "package": "BiocParallel",
      "role": "Imports"
    },
    {
      "package": "matrixStats",
      "role": "Imports"
    },
    {
      "package": "Biostrings",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "IRanges",
      "role": "Imports"
    },
    {
      "package": "Seqinfo",
      "role": "Imports"
    },
    {
      "package": "GenomeInfoDb",
      "role": "Imports"
    },
    {
      "package": "GenomicRanges",
      "role": "Imports"
    },
    {
      "package": "GenomicFiles",
      "role": "Imports"
    },
    {
      "package": "GenomicAlignments",
      "role": "Imports"
    },
    {
      "package": "GenomicFeatures",
      "role": "Imports"
    },
    {
      "package": "Rsamtools",
      "role": "Imports"
    },
    {
      "package": "AnnotationHub",
      "role": "Imports"
    },
    {
      "package": "RColorBrewer",
      "role": "Imports"
    },
    {
      "package": "AnnotationDbi",
      "role": "Imports"
    },
    {
      "package": "bitops",
      "role": "Imports"
    },
    {
      "package": "plotrix",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "cli",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "RUnit",
      "role": "Suggests"
    },
    {
      "package": "TxDb.Hsapiens.UCSC.hg38.knownGene",
      "role": "Suggests"
    },
    {
      "package": "gDNAinRNAseqData",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-24",
      "n": 1
    },
    {
      "week": "2025-26",
      "n": 2
    },
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2025-50",
      "n": 2
    },
    {
      "week": "2026-16",
      "n": 1
    },
    {
      "week": "2026-18",
      "n": 3
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.11.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.10.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "transcription",
    "transcriptomics",
    "rnaseq",
    "sequencing",
    "preprocessing",
    "software",
    "geneexpression",
    "coverage",
    "differentialexpression",
    "functionalgenomics",
    "splicedalignment",
    "alignment"
  ],
  "_stars": 2,
  "_contributors": [
    {
      "user": "rcastelo",
      "count": 51,
      "uuid": 1677433
    },
    {
      "user": "beacalvo",
      "count": 48,
      "uuid": 45432116
    },
    {
      "user": "jwokaty",
      "count": 10,
      "uuid": 1744257
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 316,
    "source": "https://www.bioconductor.org/packages/stats/bioc/gDNAx"
  },
  "_devurl": "https://github.com/functionalgenomics/gdnax",
  "_searchresults": 11,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/gDNAx.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/rcastelo/gdnax",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "allStrandModes",
    "classifyStrandMode",
    "filterBAMtx",
    "filterBAMtxFlag",
    "gDNAdx",
    "gDNAtx",
    "getDx",
    "getIgc",
    "getInt",
    "identifyStrandMode",
    "plot",
    "plotAlnOrigins",
    "plotFrgLength",
    "show",
    "singleEnd",
    "strandedness",
    "strandMode",
    "strandMode<-",
    "strnessByFeature",
    "testBAMtxFlag"
  ],
  "_help": [
    {
      "page": "gDNAx-package",
      "title": "gDNAx: diagnostics for assessing genomic DNA contamination in RNA-seq data",
      "topics": [
        "gDNAx-package",
        "gDNAx"
      ]
    },
    {
      "page": "filterBAMtx",
      "title": "Filter alignments in a BAM file using a transcriptome",
      "topics": [
        "filterBAMtx",
        "filterBAMtxFlag",
        "testBAMtxFlag"
      ]
    },
    {
      "page": "gDNAdx",
      "title": "Calculate gDNA diagnostics",
      "topics": [
        "gDNAdx",
        "plot,gDNAx,ANY-method",
        "plotAlnOrigins",
        "plotFrgLength"
      ]
    },
    {
      "page": "gDNAtx",
      "title": "Remove gDNA contamination from RNA-seq data",
      "topics": [
        "gDNAtx"
      ]
    },
    {
      "page": "gDNAx-class",
      "title": "gDNAx class",
      "topics": [
        "allStrandModes",
        "allStrandModes,gDNAx-method",
        "gDNAx-class",
        "getDx",
        "getDx,gDNAx-method",
        "getIgc",
        "getIgc,gDNAx-method",
        "getInt",
        "getInt,gDNAx-method",
        "show",
        "show,gDNAx-method",
        "singleEnd",
        "singleEnd,gDNAx-method",
        "strandedness",
        "strandedness,gDNAx-method",
        "strandMode",
        "strandMode,gDNAx-method",
        "strandMode<-",
        "strandMode<-,gDNAx-method"
      ]
    },
    {
      "page": "strandedness",
      "title": "Identify strandMode",
      "topics": [
        "classifyStrandMode",
        "identifyStrandMode",
        "strandedness,BamFileList-method",
        "strandedness,character-method",
        "strnessByFeature"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/gDNAx/raw/RELEASE_3_23/README.md",
  "_rundeps": [
    "abind",
    "AnnotationDbi",
    "AnnotationHub",
    "askpass",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocFileCache",
    "BiocGenerics",
    "BiocIO",
    "BiocManager",
    "BiocParallel",
    "BiocVersion",
    "Biostrings",
    "bit",
    "bit64",
    "bitops",
    "blob",
    "BSgenome",
    "cachem",
    "cigarillo",
    "cli",
    "codetools",
    "cpp11",
    "crayon",
    "curl",
    "DBI",
    "dbplyr",
    "DelayedArray",
    "dplyr",
    "fastmap",
    "filelock",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomeInfoDb",
    "GenomicAlignments",
    "GenomicFeatures",
    "GenomicFiles",
    "GenomicRanges",
    "glue",
    "httr",
    "httr2",
    "IRanges",
    "jsonlite",
    "KEGGREST",
    "lambda.r",
    "lattice",
    "lifecycle",
    "magrittr",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "mime",
    "openssl",
    "pillar",
    "pkgconfig",
    "plotrix",
    "png",
    "purrr",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "RCurl",
    "restfulr",
    "Rhtslib",
    "rjson",
    "rlang",
    "Rsamtools",
    "RSQLite",
    "rtracklayer",
    "S4Arrays",
    "S4Vectors",
    "Seqinfo",
    "snow",
    "SparseArray",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "UCSC.utils",
    "utf8",
    "VariantAnnotation",
    "vctrs",
    "withr",
    "XML",
    "XVector",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "gDNAx.Rmd",
      "filename": "gDNAx.html",
      "title": "The gDNAx package",
      "author": "Beatriz Calvo-Serra, Robert Castelo",
      "engine": "knitr::rmarkdown",
      "headings": [
        "What is genomic DNA contamination in a RNA-seq experiment",
        "Diagnose gDNA contamination",
        "Strandedness estimation",
        "Remove gDNA contamination",
        "Session information",
        "References"
      ],
      "created": "2023-03-16 15:44:52",
      "modified": "2025-04-14 16:56:59",
      "commits": 19
    }
  ],
  "_score": 5.1205739312058505,
  "_indexed": false,
  "_nocasepkg": "gdnax",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://bioc.r-universe.dev/gDNAx",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.10.0",
      "date": "2026-06-04T07:17:27.000Z",
      "distro": "noble",
      "commit": "fccf1b0ad2c1cbed6df21b2d1206092f155bccdb",
      "fileid": "d1213417cde6890e9bd23a4e4d78ba5170459a3e105ddb6da258a9dba64f5309",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26936490411"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.10.0",
      "date": "2026-06-04T07:17:23.000Z",
      "distro": "noble",
      "commit": "fccf1b0ad2c1cbed6df21b2d1206092f155bccdb",
      "fileid": "9d69c7dd1cf9f27b7d7ff7df9f0914dd9b833a30e1c6203c8e8317b9ebcba119",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26936490411"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.10.0",
      "date": "2026-06-04T07:16:29.000Z",
      "commit": "fccf1b0ad2c1cbed6df21b2d1206092f155bccdb",
      "fileid": "b014231ad64a91fab07c0540c2023ab4535ef803f932985a3aae4090e06692ad",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26936490411"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.10.0",
      "date": "2026-06-04T07:16:17.000Z",
      "commit": "fccf1b0ad2c1cbed6df21b2d1206092f155bccdb",
      "fileid": "6acafda372fcb0d387879905d8d2ab829c316d3f7ab6321e79cdac4a80c3046d",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26936490411"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.10.0",
      "date": "2026-06-04T07:16:44.000Z",
      "commit": "fccf1b0ad2c1cbed6df21b2d1206092f155bccdb",
      "fileid": "e0dde2a2b585fdbc22b30c85159dc3feca780a1e46865a270c1a80eca71d1802",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26936490411"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.10.0",
      "date": "2026-06-04T07:15:42.000Z",
      "commit": "fccf1b0ad2c1cbed6df21b2d1206092f155bccdb",
      "fileid": "f9ff88ada2a71d98bf6c822d51ea7a483932dba4cae2682ff4420ce327527226",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26936490411"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.10.0",
      "date": "2026-06-04T07:15:24.000Z",
      "commit": "fccf1b0ad2c1cbed6df21b2d1206092f155bccdb",
      "fileid": "c4aa16d866a8e7f3c6740c48a1b71114df07cecc1693d75f5f6ef1781c42b030",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26936490411"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.10.0",
      "date": "2026-06-04T07:15:24.000Z",
      "commit": "fccf1b0ad2c1cbed6df21b2d1206092f155bccdb",
      "fileid": "9768cd647625db89ad57c98e1cb2c8404e2bd8e5eebf70555c9df977deea09ba",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26936490411"
    }
  ]
}