{
  "_id": "6a1735f8acfb0bcc41d94da6",
  "Package": "tximeta",
  "Version": "1.31.2",
  "Title": "Transcript Quantification Import with Automatic Metadata",
  "Description": "Transcript quantification import from Salmon and other\nquantifiers with automatic attachment of transcript ranges and\nrelease information, and other associated metadata. De novo\ntranscriptomes can be linked to the appropriate sources with\nlinkedTxomes and shared for computational reproducibility.",
  "Authors@R": "c(\nperson(\"Michael\", \"Love\", email=\"michaelisaiahlove@gmail.com\", role = c(\"aut\",\"cre\")),\nperson(\"Charlotte\", \"Soneson\", role = c(\"aut\",\"ctb\")),\nperson(\"Peter\", \"Hickey\", role = c(\"aut\",\"ctb\")),\nperson(\"Rob\", \"Patro\", role = c(\"aut\",\"ctb\")),\nperson(\"NIH NHGRI\", role=\"fnd\"),\nperson(\"CZI\", role=\"fnd\")\n)",
  "Maintainer": "Michael Love <michaelisaiahlove@gmail.com>",
  "License": "GPL-2",
  "VignetteBuilder": "knitr, rmarkdown",
  "URL": "https://thelovelab.github.io/tximeta,\nhttps://github.com/thelovelab/tximeta",
  "biocViews": "Annotation, GenomeAnnotation, DataImport, Preprocessing,\nRNASeq, LongRead, SingleCell, Transcriptomics, Transcription,\nGeneExpression, FunctionalGenomics, ReproducibleResearch,\nReportWriting, ImmunoOncology",
  "Roxygen": "list(markdown = TRUE)",
  "Encoding": "UTF-8",
  "Config/Needs/website": "r-lib/pkgdown",
  "Config/roxygen2/version": "8.0.0",
  "Config/pak/sysreqs": "make libbz2-dev libicu-dev liblzma-dev libpng-dev\nlibxml2-dev libssl-dev xz-utils zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-05-27 15:10:53 UTC",
  "RemoteUrl": "https://github.com/bioc/tximeta",
  "RemoteRef": "HEAD",
  "RemoteSha": "d9a028e53c6f687abd621957e353ad6fb0f58b1c",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-27 18:07:51 UTC",
    "User": "root"
  },
  "Author": "Michael Love [aut, cre],\nCharlotte Soneson [aut, ctb],\nPeter Hickey [aut, ctb],\nRob Patro [aut, ctb],\nNIH NHGRI [fnd],\nCZI [fnd]",
  "MD5sum": "56af3293b59f9dc399525d7a02da7fd7",
  "_user": "bioc",
  "_type": "src",
  "_file": "tximeta_1.31.2.tar.gz",
  "_fileid": "2a79c3f22051392049324d91431200f201dfc4ec6b6f00f6c0ed2686a37c111b",
  "_filesize": 1948950,
  "_sha256": "2a79c3f22051392049324d91431200f201dfc4ec6b6f00f6c0ed2686a37c111b",
  "_created": "2026-05-27T18:07:51.000Z",
  "_published": "2026-05-27T18:20:40.147Z",
  "_jobs": [
    {
      "job": 78142504368,
      "time": 272,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7248211972"
    },
    {
      "job": 78142504475,
      "time": 701,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7248369186"
    },
    {
      "job": 78142504340,
      "time": 646,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7248349655"
    },
    {
      "job": 78142504374,
      "time": 419,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7248266674"
    },
    {
      "job": 78142504388,
      "time": 454,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7248279237"
    },
    {
      "job": 78141014795,
      "time": 481,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7248110495"
    },
    {
      "job": 78142504425,
      "time": 228,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7248195671"
    },
    {
      "job": 78142504366,
      "time": 617,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7248339027"
    },
    {
      "job": 78142504444,
      "time": 554,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7248316407"
    },
    {
      "job": 78142504502,
      "time": 664,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7248355858"
    }
  ],
  "_bioccheck": {
    "error": 2,
    "warning": 1,
    "note": 13
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26529170312",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/tximeta",
  "_commit": {
    "id": "d9a028e53c6f687abd621957e353ad6fb0f58b1c",
    "author": "Mike Love <mikelove@users.noreply.github.com>",
    "committer": "Mike Love <mikelove@users.noreply.github.com>",
    "message": "Merge branch 'devel' of github.com:thelovelab/tximeta into devel\n",
    "time": 1779894653
  },
  "_maintainer": {
    "name": "Michael Love",
    "email": "michaelisaiahlove@gmail.com",
    "login": "mikelove",
    "mastodon": "@mikelove@genomic.social",
    "description": "Genetics & Biostatistics at UNC-Chapel Hill. R/Bioconductor developer",
    "uuid": 69203
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.1.0",
      "role": "Depends"
    },
    {
      "package": "SummarizedExperiment",
      "version": ">= 1.39.1",
      "role": "Imports"
    },
    {
      "package": "tximport",
      "role": "Imports"
    },
    {
      "package": "jsonlite",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "IRanges",
      "role": "Imports"
    },
    {
      "package": "GenomicRanges",
      "version": ">= 1.61.1",
      "role": "Imports"
    },
    {
      "package": "AnnotationDbi",
      "role": "Imports"
    },
    {
      "package": "DBI",
      "role": "Imports"
    },
    {
      "package": "GenomicFeatures",
      "role": "Imports"
    },
    {
      "package": "txdbmaker",
      "role": "Imports"
    },
    {
      "package": "ensembldb",
      "role": "Imports"
    },
    {
      "package": "BiocFileCache",
      "role": "Imports"
    },
    {
      "package": "AnnotationHub",
      "role": "Imports"
    },
    {
      "package": "Biostrings",
      "role": "Imports"
    },
    {
      "package": "tibble",
      "role": "Imports"
    },
    {
      "package": "Seqinfo",
      "role": "Imports"
    },
    {
      "package": "tools",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "Matrix",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "tximportData",
      "version": ">= 1.37.5",
      "role": "Suggests"
    },
    {
      "package": "org.Dm.eg.db",
      "role": "Suggests"
    },
    {
      "package": "DESeq2",
      "role": "Suggests"
    },
    {
      "package": "edgeR",
      "version": ">= 4.9.2",
      "role": "Suggests"
    },
    {
      "package": "limma",
      "role": "Suggests"
    },
    {
      "package": "devtools",
      "role": "Suggests"
    },
    {
      "package": "macrophage",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 1,
  "_updates": [
    {
      "week": "2025-37",
      "n": 4
    },
    {
      "week": "2025-39",
      "n": 15
    },
    {
      "week": "2025-40",
      "n": 17
    },
    {
      "week": "2025-41",
      "n": 8
    },
    {
      "week": "2025-42",
      "n": 2
    },
    {
      "week": "2025-46",
      "n": 4
    },
    {
      "week": "2025-47",
      "n": 3
    },
    {
      "week": "2025-49",
      "n": 1
    },
    {
      "week": "2025-50",
      "n": 10
    },
    {
      "week": "2025-51",
      "n": 4
    },
    {
      "week": "2026-02",
      "n": 1
    },
    {
      "week": "2026-04",
      "n": 3
    },
    {
      "week": "2026-06",
      "n": 2
    },
    {
      "week": "2026-10",
      "n": 1
    },
    {
      "week": "2026-14",
      "n": 1
    },
    {
      "week": "2026-16",
      "n": 4
    },
    {
      "week": "2026-18",
      "n": 2
    },
    {
      "week": "2026-21",
      "n": 1
    },
    {
      "week": "2026-22",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.31.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.30.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "annotation",
    "genomeannotation",
    "dataimport",
    "preprocessing",
    "rnaseq",
    "longread",
    "singlecell",
    "transcriptomics",
    "transcription",
    "geneexpression",
    "functionalgenomics",
    "reproducibleresearch",
    "reportwriting",
    "immunooncology"
  ],
  "_stars": 72,
  "_contributors": [
    {
      "user": "mikelove",
      "count": 488,
      "uuid": 69203
    },
    {
      "user": "jwokaty",
      "count": 16,
      "uuid": 1744257
    },
    {
      "user": "nturaga",
      "count": 14,
      "uuid": 2746443
    },
    {
      "user": "csoneson",
      "count": 9,
      "uuid": 5628952
    },
    {
      "user": "hpages",
      "count": 2,
      "uuid": 8810451
    },
    {
      "user": "vobencha",
      "count": 2,
      "uuid": 2466173
    },
    {
      "user": "plbaldoni",
      "count": 1,
      "uuid": 26856909
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 2760,
    "source": "https://www.bioconductor.org/packages/stats/bioc/tximeta"
  },
  "_mentions": 11,
  "_devurl": "https://github.com/thelovelab/tximeta",
  "_pkgdown": "https://thelovelab.github.io/tximeta",
  "_searchresults": 584,
  "_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/readme.html",
    "extra/readme.md",
    "extra/tximeta.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/thelovelab/tximeta",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "addCDS",
    "addExons",
    "addIds",
    "getTximetaBFC",
    "importData",
    "inspectDigests",
    "loadLinkedTxome",
    "makeDGEList",
    "makeLinkedTxome",
    "makeLinkedTxpData",
    "retrieveCDNA",
    "retrieveDb",
    "setTximetaBFC",
    "splitSE",
    "summarizeToGene",
    "tximeta",
    "updateMetadata"
  ],
  "_help": [
    {
      "page": "tximeta-package",
      "title": "Import transcript quantification with metadata",
      "topics": [
        "tximeta-package"
      ]
    },
    {
      "page": "addCDS",
      "title": "Add CDS to rowRanges of a transcript-level SummarizedExperiment",
      "topics": [
        "addCDS"
      ]
    },
    {
      "page": "addExons",
      "title": "Add exons to rowRanges of a transcript-level SummarizedExperiment",
      "topics": [
        "addExons"
      ]
    },
    {
      "page": "addIds",
      "title": "Add IDs to rowRanges of a SummarizedExperiment",
      "topics": [
        "addIds"
      ]
    },
    {
      "page": "getTximetaBFC",
      "title": "Get or set the directory of the BiocFileCache used by tximeta",
      "topics": [
        "getTximetaBFC",
        "setTximetaBFC"
      ]
    },
    {
      "page": "importData",
      "title": "Import quantification across mixed reference transcripts",
      "topics": [
        "importData"
      ]
    },
    {
      "page": "inspectDigests",
      "title": "Inspect digest matches from 'importData()' imported data",
      "topics": [
        "inspectDigests"
      ]
    },
    {
      "page": "linkedTxome",
      "title": "Make and load linked transcriptomes (linked GTF and FASTA)",
      "topics": [
        "linkedTxome",
        "loadLinkedTxome",
        "makeLinkedTxome"
      ]
    },
    {
      "page": "linkedTxpData",
      "title": "Make linked transcript data (linked GRanges)",
      "topics": [
        "linkedTxpData",
        "makeLinkedTxpData"
      ]
    },
    {
      "page": "makeDGEList",
      "title": "Make a DGEList from tximeta output",
      "topics": [
        "makeDGEList"
      ]
    },
    {
      "page": "retrieveCDNA",
      "title": "Retrieve the cDNA transcript sequence for a SummarizedExperiment",
      "topics": [
        "retrieveCDNA"
      ]
    },
    {
      "page": "retrieveDb",
      "title": "Retrieve the TxDb or EnsDb associated with a SummarizedExperiment",
      "topics": [
        "retrieveDb"
      ]
    },
    {
      "page": "splitSE",
      "title": "Split SummarizedExperiment by gene categories",
      "topics": [
        "splitSE"
      ]
    },
    {
      "page": "summarizeToGene",
      "title": "Summarize estimated quantitites to gene-level",
      "topics": [
        "summarizeToGene,SummarizedExperiment-method"
      ]
    },
    {
      "page": "tximeta",
      "title": "Import transcript quantification with metadata",
      "topics": [
        "tximeta"
      ]
    },
    {
      "page": "updateMetadata",
      "title": "Update transcript metadatda for 'importData()' imported data",
      "topics": [
        "updateMetadata"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/tximeta/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "AnnotationDbi",
    "AnnotationFilter",
    "AnnotationHub",
    "askpass",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocFileCache",
    "BiocGenerics",
    "BiocIO",
    "BiocManager",
    "BiocParallel",
    "BiocVersion",
    "biomaRt",
    "Biostrings",
    "bit",
    "bit64",
    "bitops",
    "blob",
    "cachem",
    "cigarillo",
    "cli",
    "codetools",
    "cpp11",
    "crayon",
    "curl",
    "DBI",
    "dbplyr",
    "DelayedArray",
    "dplyr",
    "ensembldb",
    "fastmap",
    "filelock",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomeInfoDb",
    "GenomicAlignments",
    "GenomicFeatures",
    "GenomicRanges",
    "glue",
    "hms",
    "httr",
    "httr2",
    "IRanges",
    "jsonlite",
    "KEGGREST",
    "lambda.r",
    "lattice",
    "lazyeval",
    "lifecycle",
    "magrittr",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "mime",
    "openssl",
    "pillar",
    "pkgconfig",
    "png",
    "prettyunits",
    "progress",
    "ProtGenerics",
    "purrr",
    "R6",
    "rappdirs",
    "RCurl",
    "restfulr",
    "Rhtslib",
    "rjson",
    "rlang",
    "Rsamtools",
    "RSQLite",
    "rtracklayer",
    "S4Arrays",
    "S4Vectors",
    "Seqinfo",
    "snow",
    "SparseArray",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "txdbmaker",
    "tximport",
    "UCSC.utils",
    "utf8",
    "vctrs",
    "withr",
    "XML",
    "xml2",
    "XVector",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "tximeta.Rmd",
      "filename": "tximeta.html",
      "title": "tximeta: transcript quantification import with automatic metadata",
      "author": "Michael I. Love, Charlotte Soneson, Peter F. Hickey, Rob Patro",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Preparing tximeta input",
        "Running tximeta",
        "How does it work?",
        "Packages used for caching metadata",
        "Pre-computed digests",
        "SummarizedExperiment output",
        "Retrieve the transcript database",
        "Add exons per transcript",
        "Easy summarization to gene-level",
        "Assign ranges by abundance",
        "Add different identifiers",
        "Differential gene expression analysis",
        "Differential transcript expression and usage analysis",
        "Additional metadata slots",
        "Mixed reference transcripts",
        "Errors connecting to a database",
        "What if digest isn't known?",
        "Linked transcriptomes",
        "Clear linkedTxomes",
        "Loading linkedTxome JSON files",
        "Clear linkedTxomes again",
        "alevin details",
        "Other quantifiers",
        "Acknowledgments",
        "Session info",
        "References"
      ],
      "created": "2018-07-12 07:53:35",
      "modified": "2026-05-27 15:10:53",
      "commits": 91
    }
  ],
  "_score": 11.29765053600104,
  "_indexed": true,
  "_nocasepkg": "tximeta",
  "_universes": [
    "bioc",
    "mikelove",
    "thelovelab"
  ],
  "_previous": "1.31.0",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.31.2",
      "date": "2026-05-27T18:13:35.000Z",
      "distro": "noble",
      "commit": "d9a028e53c6f687abd621957e353ad6fb0f58b1c",
      "fileid": "32a15c8489aa6015e6870354e8520c37e40e85d9f52fa217fe8afc0839dd6329",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26529170312"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.31.2",
      "date": "2026-05-27T18:12:57.000Z",
      "distro": "noble",
      "commit": "d9a028e53c6f687abd621957e353ad6fb0f58b1c",
      "fileid": "047885f4e34d5cf062631c09bf7895af54616517abb2178504fb269c8e892865",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26529170312"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.31.2",
      "date": "2026-05-27T18:10:24.000Z",
      "commit": "d9a028e53c6f687abd621957e353ad6fb0f58b1c",
      "fileid": "d9a8dea133ece520ba62aead74bb40da9a34d428e22ad697aaf707af194ae93c",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26529170312"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.31.2",
      "date": "2026-05-27T18:10:52.000Z",
      "commit": "d9a028e53c6f687abd621957e353ad6fb0f58b1c",
      "fileid": "e603fdecce3a146d908988a935f2ad8367b4ba4ca575545d2f89ec6f2fff5c29",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26529170312"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.31.2",
      "date": "2026-05-27T18:12:22.000Z",
      "commit": "d9a028e53c6f687abd621957e353ad6fb0f58b1c",
      "fileid": "66d5e7f57aa097d3cbea808f984db6c3918b2f775d01677fd7478e354740aa9a",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26529170312"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.31.2",
      "date": "2026-05-27T18:11:31.000Z",
      "commit": "d9a028e53c6f687abd621957e353ad6fb0f58b1c",
      "fileid": "dd72b105490aa26d4810dba7d0af1fa3257d67f788368008542683097b357cfa",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26529170312"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.31.2",
      "date": "2026-05-27T18:10:37.000Z",
      "commit": "d9a028e53c6f687abd621957e353ad6fb0f58b1c",
      "fileid": "d4b73bd4b01912469a4214cd5353214a36f2de33e3b2e819bbed350409ac7904",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26529170312"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.31.2",
      "date": "2026-05-27T18:11:09.000Z",
      "commit": "d9a028e53c6f687abd621957e353ad6fb0f58b1c",
      "fileid": "bb6f57cfb8320d49b516510cb0cfbfbfff4374904b474f4d5668f610ececaf27",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26529170312"
    }
  ]
}