{
  "_id": "6a498f566d67900babdfb6df",
  "Package": "tximport",
  "Version": "1.41.0",
  "Title": "Import and summarize transcript-level estimates for transcript-\nand gene-level analysis",
  "Description": "Imports transcript-level abundance, estimated counts and\ntranscript lengths, and summarizes into matrices for use with\ndownstream gene-level analysis packages. Average transcript\nlength, weighted by sample-specific transcript abundance\nestimates, is provided as a matrix which can be used as an\noffset for different expression of gene-level counts.",
  "Author": "Michael Love [cre,aut], Charlotte Soneson [aut], Mark Robinson\n[aut], Rob Patro [ctb], Andrew Parker Morgan [ctb], Ryan C.\nThompson [ctb], Matt Shirley [ctb], Avi Srivastava [ctb]",
  "Maintainer": "Michael Love <michaelisaiahlove@gmail.com>",
  "License": "LGPL (>=2)",
  "VignetteBuilder": "knitr",
  "URL": "https://github.com/thelovelab/tximport",
  "biocViews": "DataImport, Preprocessing, RNASeq, Transcriptomics,\nTranscription, GeneExpression, ImmunoOncology",
  "RoxygenNote": "7.2.3",
  "NeedsCompilation": "no",
  "Encoding": "UTF-8",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:42:36 UTC",
  "RemoteUrl": "https://github.com/bioc/tximport",
  "RemoteRef": "HEAD",
  "RemoteSha": "5feefe5f2603a5f8aea3981ee756e25befeae9a5",
  "Packaged": {
    "Date": "2026-07-04 22:44:35 UTC",
    "User": "root"
  },
  "_user": "bioc",
  "_type": "src",
  "_file": "tximport_1.41.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/c7f0e04d1331e34bb3cdc03bfb4efd5c9e42fa27ddfa4904298ed2718caff52c",
  "_filesize": 176851,
  "_sha256": "c7f0e04d1331e34bb3cdc03bfb4efd5c9e42fa27ddfa4904298ed2718caff52c",
  "_expires": "2026-10-12T22:55:16.000Z",
  "_created": "2026-07-04T22:44:35.000Z",
  "_published": "2026-07-04T22:55:18.725Z",
  "_bioccheck": {
    "error": 2,
    "warning": 1,
    "note": 9
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28721926724",
  "_status": "success",
  "_upstream": "https://github.com/bioc/tximport",
  "_commit": {
    "id": "5feefe5f2603a5f8aea3981ee756e25befeae9a5",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777380156
  },
  "_maintainer": {
    "name": "Michael Love",
    "email": "michaelisaiahlove@gmail.com",
    "login": "mikelove",
    "mastodon": "@mikelove@genomic.social",
    "orcid": "0000-0001-8401-0545",
    "description": "Genetics & Biostatistics at UNC-Chapel Hill. R/Bioconductor developer",
    "uuid": 69203
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 85173166548,
      "time": 224,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "8086120212"
    },
    {
      "job": 85173166556,
      "time": 332,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8086131836"
    },
    {
      "job": 85173166551,
      "time": 310,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8086129404"
    },
    {
      "job": 85173166559,
      "time": 137,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8086122559"
    },
    {
      "job": 85173166558,
      "time": 154,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8086125235"
    },
    {
      "job": 85172844853,
      "time": 331,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8086095566"
    },
    {
      "job": 85173166540,
      "time": 222,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8086119838"
    },
    {
      "job": 85173166561,
      "time": 605,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8086161898"
    },
    {
      "job": 85173166552,
      "time": 586,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8086159970"
    },
    {
      "job": 85173166581,
      "time": 578,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8086159217"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "tximportData",
      "role": "Suggests"
    },
    {
      "package": "TxDb.Hsapiens.UCSC.hg19.knownGene",
      "role": "Suggests"
    },
    {
      "package": "readr",
      "version": ">= 0.2.2",
      "role": "Suggests"
    },
    {
      "package": "arrow",
      "role": "Suggests"
    },
    {
      "package": "limma",
      "role": "Suggests"
    },
    {
      "package": "edgeR",
      "version": ">= 4.9.2",
      "role": "Suggests"
    },
    {
      "package": "DESeq2",
      "version": ">= 1.11.6",
      "role": "Suggests"
    },
    {
      "package": "rhdf5",
      "role": "Suggests"
    },
    {
      "package": "jsonlite",
      "role": "Suggests"
    },
    {
      "package": "matrixStats",
      "role": "Suggests"
    },
    {
      "package": "Matrix",
      "role": "Suggests"
    },
    {
      "package": "eds",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 12,
  "_updates": [
    {
      "week": "2025-27",
      "n": 3
    },
    {
      "week": "2025-33",
      "n": 1
    },
    {
      "week": "2025-34",
      "n": 1
    },
    {
      "week": "2025-40",
      "n": 1
    },
    {
      "week": "2026-16",
      "n": 5
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.41.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.40.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "dataimport",
    "preprocessing",
    "rnaseq",
    "transcriptomics",
    "transcription",
    "geneexpression",
    "immunooncology",
    "bioconductor",
    "deseq2"
  ],
  "_stars": 145,
  "_contributors": [
    {
      "user": "mikelove",
      "count": 276,
      "uuid": 69203
    },
    {
      "user": "nturaga",
      "count": 14,
      "uuid": 2746443
    },
    {
      "user": "jwokaty",
      "count": 14,
      "uuid": 1744257
    },
    {
      "user": "rob-p",
      "count": 6,
      "uuid": 361470
    },
    {
      "user": "dtenenba",
      "count": 4,
      "uuid": 2286826
    },
    {
      "user": "atpoint",
      "count": 3,
      "uuid": 21218078
    },
    {
      "user": "hpages",
      "count": 2,
      "uuid": 8810451
    },
    {
      "user": "vobencha",
      "count": 2,
      "uuid": 2466173
    },
    {
      "user": "ltla",
      "count": 1,
      "uuid": 8166669
    },
    {
      "user": "mdshw5",
      "count": 1,
      "uuid": 819554
    },
    {
      "user": "roryk",
      "count": 1,
      "uuid": 414586
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 445,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_mentions": 367,
  "_devurl": "https://github.com/thelovelab/tximport",
  "_searchresults": 5576,
  "_rbuild": "4.6.1",
  "_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/tximport.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/thelovelab/tximport",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "makeCountsFromAbundance",
    "summarizeToGene",
    "tximport"
  ],
  "_help": [
    {
      "page": "tximport-package",
      "title": "Tximport package: import transcript-level quantification data",
      "topics": [
        "tximport-package"
      ]
    },
    {
      "page": "makeCountsFromAbundance",
      "title": "Low-level function to make counts from abundance using matrices",
      "topics": [
        "makeCountsFromAbundance"
      ]
    },
    {
      "page": "summarizeToGene",
      "title": "Summarize estimated quantitites to gene-level",
      "topics": [
        "summarizeToGene",
        "summarizeToGene,list-method"
      ]
    },
    {
      "page": "tximport",
      "title": "Import transcript-level abundances and counts for transcript- and gene-level analysis packages",
      "topics": [
        "tximport"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/tximport/raw/HEAD/README.md",
  "_rundeps": [],
  "_vignettes": [
    {
      "source": "tximport.Rmd",
      "filename": "tximport.html",
      "title": "Importing transcript abundance with tximport",
      "author": "Michael I. Love, Charlotte Soneson, Mark D. Robinson",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Import transcript-level estimates",
        "salmon",
        "salmon with inferential replicates",
        "kallisto",
        "kallisto with inferential replicates",
        "kallisto with TSV files",
        "RSEM",
        "StringTie",
        "alevin",
        "oarfish",
        "Downstream DGE in Bioconductor",
        "3' tagged RNA-seq",
        "DESeq2",
        "edgeR",
        "limma-voom",
        "Acknowledgments",
        "Session info",
        "References"
      ],
      "created": "2015-12-01 15:29:59",
      "modified": "2026-04-13 16:35:50",
      "commits": 49
    }
  ],
  "_score": 12.941114522811878,
  "_indexed": true,
  "_nocasepkg": "tximport",
  "_universes": [
    "bioc",
    "mikelove",
    "thelovelab"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.41.0",
      "date": "2026-07-04T22:49:04.000Z",
      "distro": "resolute",
      "commit": "5feefe5f2603a5f8aea3981ee756e25befeae9a5",
      "fileid": "https://r2.ropensci.org/48d11aa41d96470bea0da2c597d2f2068bd765f758ddc13be2ab8afa9961b778",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28721926724"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.41.0",
      "date": "2026-07-04T22:48:40.000Z",
      "distro": "resolute",
      "commit": "5feefe5f2603a5f8aea3981ee756e25befeae9a5",
      "fileid": "https://r2.ropensci.org/33831ef912720baf625abc286db318f7b743dac6ff31eeb1d8af384d8a94e4e2",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28721926724"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.41.0",
      "date": "2026-07-04T22:48:05.000Z",
      "commit": "5feefe5f2603a5f8aea3981ee756e25befeae9a5",
      "fileid": "https://r2.ropensci.org/bc052945595b948ed3b4e0525b6e03916b46e5cc94a1f1610f4a4dcdf82f308e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28721926724"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.41.0",
      "date": "2026-07-04T22:48:27.000Z",
      "commit": "5feefe5f2603a5f8aea3981ee756e25befeae9a5",
      "fileid": "https://r2.ropensci.org/e06ee5c7fcf1a6962af2399938eacc83bb56a6d94640beba4d00c7a8c0fca700",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28721926724"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.41.0",
      "date": "2026-07-04T22:48:29.000Z",
      "commit": "5feefe5f2603a5f8aea3981ee756e25befeae9a5",
      "fileid": "https://r2.ropensci.org/b1208f29621ca7973e9e546e16ca0010334244a18720b56f85ea3ee38bac8eeb",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28721926724"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.41.0",
      "date": "2026-07-04T22:53:28.000Z",
      "commit": "5feefe5f2603a5f8aea3981ee756e25befeae9a5",
      "fileid": "https://r2.ropensci.org/7f0e01af4eb72b51ddaf4cb989ea81663f98d647ef294df29c5d0d50d585084d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28721926724"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.41.0",
      "date": "2026-07-04T22:53:13.000Z",
      "commit": "5feefe5f2603a5f8aea3981ee756e25befeae9a5",
      "fileid": "https://r2.ropensci.org/2bb4300b47cec48a103f6382984cb0c2a8c61ba934903ab51f425b14d2fa5bee",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28721926724"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.41.0",
      "date": "2026-07-04T22:53:01.000Z",
      "commit": "5feefe5f2603a5f8aea3981ee756e25befeae9a5",
      "fileid": "https://r2.ropensci.org/8d6f67ad84509c43d93957452011bc15fbbd029f354d6047aa835fd7bf8faf9e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28721926724"
    }
  ]
}