{ "_id": "6ae2fb653d0f299392dd05b0", "Package": "tximport", "Version": "1.41.1", "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": "7.3.3", "NeedsCompilation": "no", "Encoding": "UTF-8", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-09-28 14:43:52 UTC", "RemoteUrl": "https://github.com/bioc/tximport", "RemoteRef": "HEAD", "RemoteSha": "2c532670e2f58139a7ebc3a57fd2ccf22d5b8cdf", "Packaged": { "Date": "2026-10-29 07:43:24 UTC", "User": "root" }, "_user": "bioc", "_type": "src", "_file": "tximport_1.41.1.tar.gz", "_fileid": "https://r2.ropensci.org/4a1a6941596d485bc3ed733eed22d6866edb9a8ecd268e172b61aee2e5cf7168", "_filesize": 164314, "_sha256": "4a1a6941596d485bc3ed733eed22d6866edb9a8ecd268e172b61aee2e5cf7168", "_expires": "2027-02-06T07:53:07.000Z", "_created": "2026-10-29T07:43:24.000Z", "_published": "2026-10-29T07:53:09.485Z", "_upstream": "https://github.com/bioc/tximport", "_status": "success", "_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 }, "_jobs": [ { "job": 123324966042, "time": 270, "config": "bioc-checks", "r": "4.6.1", "check": "ERROR", "artifact": "12880494753" }, { "job": 123324966072, "time": 333, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12881780573" }, { "job": 123324966112, "time": 448, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12881865565" }, { "job": 123324965994, "time": 329, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "12881337063" }, { "job": 123324966071, "time": 209, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "12880654995" }, { "job": 123322066154, "time": 479, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "12881037535" }, { "job": 123324966023, "time": 298, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "12881327712" }, { "job": 123324966066, "time": 520, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12880934324" }, { "job": 123324966130, "time": 507, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "12881577531" }, { "job": 123324966254, "time": 543, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12881771085" } ], "_bioccheck": { "error": 2, "warning": 1, "note": 10 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/40836127660", "_commit": { "id": "2c532670e2f58139a7ebc3a57fd2ccf22d5b8cdf", "author": "Mike Love ", "committer": "Mike Love ", "message": "merge\n", "time": 1790606632 }, "_distro": "resolute", "_host": "GitHub-Actions", "_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", "version": ">= 1.41.1", "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": "2026-16", "n": 6 }, { "week": "2026-40", "n": 3 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.41.1", "bioc": "3.24", "repository": "bioc" }, { "branch": "release", "version": "1.40.0", "bioc": "3.23", "repository": "bioc" } ], "_topics": [ "dataimport", "preprocessing", "rnaseq", "transcriptomics", "transcription", "geneexpression", "immunooncology", "bioconductor", "deseq2" ], "_stars": 146, "_contributors": [ { "user": "mikelove", "count": 279, "uuid": 69203 }, { "user": "jwokaty", "count": 16, "uuid": 1744257 }, { "user": "nturaga", "count": 14, "uuid": 2746443 }, { "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": 480, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 8604, "source": "https://www.bioconductor.org/packages/stats/bioc/tximport" }, "_mentions": 367, "_devurl": "https://github.com/thelovelab/tximport", "_searchresults": 4488, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "extra/tximport.html" ], "_homeurl": "https://github.com/thelovelab/tximport", "_realowner": "bioc", "_cranurl": false, "_exports": [ "makeCountsFromAbundance", "summarizeToGene", "tximport" ], "_help": [ { "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 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": "2026-09-28 14:40:58", "commits": 50 } ], "_score": 13.342170712774465, "_indexed": true, "_nocasepkg": "tximport", "_universes": [ "bioc", "mikelove", "thelovelab" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.41.1", "date": "2026-10-29T07:48:05.000Z", "distro": "resolute", "commit": "2c532670e2f58139a7ebc3a57fd2ccf22d5b8cdf", "fileid": "https://r2.ropensci.org/3c25a7eebd81c8e195fa72e31fe0a421ea881bdaaef60ced498438218304f4e4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/40836127660" }, { "r": "4.6.1", "os": "linux", "version": "1.41.1", "date": "2026-10-29T07:50:13.000Z", "distro": "resolute", "commit": "2c532670e2f58139a7ebc3a57fd2ccf22d5b8cdf", "fileid": "https://r2.ropensci.org/1d9247f81ad43bda85c606cd6c8726df1d397ee4b6900508ba8d76ccff97bad5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/40836127660" }, { "r": "4.5.3", "os": "mac", "version": "1.41.1", "date": "2026-10-29T07:48:12.000Z", "commit": "2c532670e2f58139a7ebc3a57fd2ccf22d5b8cdf", "fileid": "https://r2.ropensci.org/0191273054990365b3683773fb28b8b072dd3bfdd061f7551e74063396597dbe", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/40836127660" }, { "r": "4.6.1", "os": "mac", "version": "1.41.1", "date": "2026-10-29T07:45:59.000Z", "commit": "2c532670e2f58139a7ebc3a57fd2ccf22d5b8cdf", "fileid": "https://r2.ropensci.org/158d8ae1a2b297c1cef055e3546b922e12fbc395b378c778132e4e921caf86eb", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/40836127660" }, { "r": "4.6.0", "os": "wasm", "version": "1.41.1", "date": "2026-10-29T07:48:44.000Z", "commit": "2c532670e2f58139a7ebc3a57fd2ccf22d5b8cdf", "fileid": "https://r2.ropensci.org/b395faf3d9f56966ebea7767eb93bda1dc6e1d717343d647dedb749c880dbba5", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/40836127660" }, { "r": "4.7.0", "os": "win", "version": "1.41.1", "date": "2026-10-29T07:51:18.000Z", "commit": "2c532670e2f58139a7ebc3a57fd2ccf22d5b8cdf", "fileid": "https://r2.ropensci.org/afdf6601f02f2d259a6ebfd272e594115777552d1d4c742cf3ec1c0cd6b6191c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/40836127660" }, { "r": "4.5.3", "os": "win", "version": "1.41.1", "date": "2026-10-29T07:51:11.000Z", "commit": "2c532670e2f58139a7ebc3a57fd2ccf22d5b8cdf", "fileid": "https://r2.ropensci.org/8d370abb5ebaeb8c9d3b5701ce0c98ab33268f85661b42e0c6cfdbe36c99b38c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/40836127660" }, { "r": "4.6.1", "os": "win", "version": "1.41.1", "date": "2026-10-29T07:52:01.000Z", "commit": "2c532670e2f58139a7ebc3a57fd2ccf22d5b8cdf", "fileid": "https://r2.ropensci.org/7ef994038f7473b016bd51ba90deb008aea97cca5dfad886f8b1841141c5b415", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/40836127660" } ] }