{ "_id": "6a1af2fc1d7bb097a09f7f59", "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 ", "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": "2026-05-30 09:45:00 UTC", "User": "root" }, "MD5sum": "ec9940269e9f9c643815982b45a56d1e", "_user": "bioc", "_type": "src", "_file": "tximport_1.41.0.tar.gz", "_fileid": "60ba66eafcc088a26e13860a9a7b93c7485ff39040e76a8a4ae04fb5dac9de37", "_filesize": 176016, "_sha256": "60ba66eafcc088a26e13860a9a7b93c7485ff39040e76a8a4ae04fb5dac9de37", "_created": "2026-05-30T09:45:00.000Z", "_published": "2026-05-30T14:23:56.027Z", "_jobs": [ { "job": 78640509865, "time": 224, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7307455147" }, { "job": 78640509882, "time": 305, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7307462243" }, { "job": 78640509871, "time": 228, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7307455570" }, { "job": 78640509873, "time": 203, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7308840542" }, { "job": 78640509875, "time": 185, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7308837397" }, { "job": 78639768374, "time": 299, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7307276474" }, { "job": 78640509868, "time": 176, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7307450425" }, { "job": 78640509872, "time": 586, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7307485725" }, { "job": 78640509881, "time": 579, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7307485154" }, { "job": 78640509874, "time": 611, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7307487665" } ], "_bioccheck": { "error": 2, "warning": 1, "note": 10 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26676574099", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/tximport", "_commit": { "id": "5feefe5f2603a5f8aea3981ee756e25befeae9a5", "author": "A Wokaty ", "committer": "A Wokaty ", "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": "noble", "_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": 13, "_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", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 6756, "source": "https://www.bioconductor.org/packages/stats/bioc/tximport" }, "_mentions": 367, "_devurl": "https://github.com/thelovelab/tximport", "_searchresults": 4288, "_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/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": 13.69149828156482, "_indexed": true, "_nocasepkg": "tximport", "_universes": [ "bioc", "mikelove", "thelovelab" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.41.0", "date": "2026-05-30T10:16:51.000Z", "distro": "noble", "commit": "5feefe5f2603a5f8aea3981ee756e25befeae9a5", "fileid": "6f24f6e157d85940ae20b39f4d4557d8f55cb197bca5314e9ed0bf1af3031930", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676574099" }, { "r": "4.6.0", "os": "linux", "version": "1.41.0", "date": "2026-05-30T10:15:55.000Z", "distro": "noble", "commit": "5feefe5f2603a5f8aea3981ee756e25befeae9a5", "fileid": "49bb2343bf0db98b96bb81f272df7bc0d519b0f199f7eed3be8669d4ae359d51", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676574099" }, { "r": "4.5.3", "os": "mac", "version": "1.41.0", "date": "2026-05-30T14:22:11.000Z", "commit": "5feefe5f2603a5f8aea3981ee756e25befeae9a5", "fileid": "a9bb1662b55c0980898d3d1f66eaaf7de618df1742b38d74d691302c5f94d7bb", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676574099" }, { "r": "4.6.0", "os": "mac", "version": "1.41.0", "date": "2026-05-30T14:21:57.000Z", "commit": "5feefe5f2603a5f8aea3981ee756e25befeae9a5", "fileid": "a49e1acb3eb52b76483761635a7ffcd688301e1a073fcf194f6a7194bcec5a11", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676574099" }, { "r": "4.6.0", "os": "wasm", "version": "1.41.0", "date": "2026-05-30T10:16:01.000Z", "commit": "5feefe5f2603a5f8aea3981ee756e25befeae9a5", "fileid": "649d6ecb48579ef8af87a6fd9e192e9c13adbbe08536e64f89b4f98f46f48abd", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676574099" }, { "r": "4.7.0", "os": "win", "version": "1.41.0", "date": "2026-05-30T10:21:13.000Z", "commit": "5feefe5f2603a5f8aea3981ee756e25befeae9a5", "fileid": "eac80df7c1c1e0e206e4d843bcd30726530ff6539321a07b55f581c3dc21db9c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676574099" }, { "r": "4.5.3", "os": "win", "version": "1.41.0", "date": "2026-05-30T10:21:04.000Z", "commit": "5feefe5f2603a5f8aea3981ee756e25befeae9a5", "fileid": "b4a5d8cbbca8cc3e5645b14a3de31c95271a9ebeae9b6c6ef6fd8e7cec077102", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676574099" }, { "r": "4.6.0", "os": "win", "version": "1.41.0", "date": "2026-05-30T10:21:25.000Z", "commit": "5feefe5f2603a5f8aea3981ee756e25befeae9a5", "fileid": "cb35f646e831c3911cbcdfac3bb3a5bfcc97d99de76d02130cd577e08794d76f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676574099" } ] }