{ "_id": "6a49ce7e1b0c6c282ca7d5f5", "Package": "txcutr", "Title": "Transcriptome CUTteR", "Description": "Various mRNA sequencing library preparation methods\ngenerate sequencing reads specifically from the transcript\nends. Analyses that focus on quantification of isoform usage\nfrom such data can be aided by using truncated versions of\ntranscriptome annotations, both at the alignment or\npseudo-alignment stage, as well as in downstream analysis. This\npackage implements some convenience methods for readily\ngenerating such truncated annotations and their corresponding\nsequences.", "Version": "1.19.0", "Date": "2025-09-07", "Authors@R": "person(given = \"Mervin\",\nfamily = \"Fansler\",\nrole = c(\"aut\", \"cre\"),\nemail = \"mervin.fansler@bric.ku.dk\",\ncomment = c(ORCID = \"0000-0002-4108-4218\"))", "License": "GPL-3", "URL": "https://github.com/mfansler/txcutr", "BugReports": "https://github.com/mfansler/txcutr/issues", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.1", "biocViews": "Alignment, Annotation, RNASeq, Sequencing, Transcriptomics", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "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": "2026-04-28 12:57:25 UTC", "RemoteUrl": "https://github.com/bioc/txcutr", "RemoteRef": "HEAD", "RemoteSha": "f77e877da0650ce6b75bbc781bfd2b5f7dcd892f", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-05 02:58:39 UTC", "User": "root" }, "Author": "Mervin Fansler [aut, cre] (ORCID:\n)", "Maintainer": "Mervin Fansler ", "_user": "bioc", "_type": "src", "_file": "txcutr_1.19.0.tar.gz", "_fileid": "https://r2.ropensci.org/e2260f8ef9b344661bbc7f841a558a1bb6d8a271dbf718653df1c4b864c2635f", "_filesize": 140836, "_sha256": "e2260f8ef9b344661bbc7f841a558a1bb6d8a271dbf718653df1c4b864c2635f", "_expires": "2026-10-13T03:24:44.000Z", "_created": "2026-07-05T02:58:39.000Z", "_published": "2026-07-05T03:24:46.610Z", "_bioccheck": { "error": 0, "warning": 0, "note": 4 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28727468502", "_status": "success", "_upstream": "https://github.com/bioc/txcutr", "_commit": { "id": "f77e877da0650ce6b75bbc781bfd2b5f7dcd892f", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777381045 }, "_maintainer": { "name": "Mervin Fansler", "email": "mervin.fansler@bric.ku.dk", "login": "mfansler", "bluesky": "@mfansler.bsky.social", "linkedin": "in/mervinfansler", "orcid": "0000-0002-4108-4218", "description": "R Team @conda-forge. Postdoc in @cvejic-group BRIC, UCPH. PhD from @Mayrlab MSKCC. scUTRquant creator. Reproducible research enthusiast.", "uuid": 1182216 }, "_distro": "resolute", "_jobs": [ { "job": 85187531766, "time": 261, "config": "bioc-checks", "r": "4.6.1", "check": "NOTE", "artifact": "8087756288" }, { "job": 85187531777, "time": 610, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "8087801162" }, { "job": 85187531794, "time": 580, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "8087797077" }, { "job": 85187531773, "time": 330, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "8087764806" }, { "job": 85187531792, "time": 301, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "8087761153" }, { "job": 85187235893, "time": 340, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8087727553" }, { "job": 85187531778, "time": 242, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8087754176" }, { "job": 85187531795, "time": 1479, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "8087911422" }, { "job": 85187531791, "time": 1402, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "8087902912" }, { "job": 85187531781, "time": 1506, "config": "windows-release", "r": "4.6.1", "check": "NOTE", "artifact": "8087914001" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.5.0", "role": "Depends" }, { "package": "AnnotationDbi", "role": "Imports" }, { "package": "GenomicFeatures", "role": "Imports" }, { "package": "txdbmaker", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "GenomicRanges", "role": "Imports" }, { "package": "BiocGenerics", "role": "Imports" }, { "package": "Biostrings", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "rtracklayer", "role": "Imports" }, { "package": "BiocParallel", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "RefManageR", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "sessioninfo", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "TxDb.Scerevisiae.UCSC.sacCer3.sgdGene", "role": "Suggests" }, { "package": "BSgenome.Scerevisiae.UCSC.sacCer3", "role": "Suggests" }, { "package": "GenomeInfoDbData", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-30", "n": 1 }, { "week": "2025-36", "n": 2 }, { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.19.0", "bioc": "3.24" }, { "branch": "release", "version": "1.18.0", "bioc": "3.23" } ], "_topics": [ "alignment", "annotation", "rnaseq", "sequencing", "transcriptomics" ], "_stars": 5, "_contributors": [ { "user": "mfansler", "count": 43, "uuid": 1182216 }, { "user": "jwokaty", "count": 12, "uuid": 1744257 }, { "user": "nturaga", "count": 4, "uuid": 2746443 }, { "user": "hpages", "count": 1, "uuid": 8810451 }, { "user": "lshep", "count": 1, "uuid": 18724380 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 445, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_devurl": "https://github.com/mfansler/txcutr", "_searchresults": 10, "_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/txcutr.html", "manual.pdf" ], "_homeurl": "https://github.com/mfansler/txcutr", "_realowner": "bioc", "_cranurl": false, "_exports": [ "exportFASTA", "exportGTF", "exportMergeTable", "generateMergeTable", "truncateTxome", "txdbToGRangesList" ], "_help": [ { "page": "dot-clipTranscript", "title": "Clip Transcript to Given Length", "topics": [ ".clipTranscript" ] }, { "page": "dot-fillReduce", "title": "Convert GRanges to Single Range", "topics": [ ".fillReduce" ] }, { "page": "dot-mutateEach-CompressedGRangesList-method", "title": "Efficient Metadata Columns Mutation", "topics": [ ".mutateEach,CompressedGRangesList-method" ] }, { "page": "dot-propagateMap", "title": "Propagate Transcript Merge Map", "topics": [ ".propagateMap" ] }, { "page": "exportFASTA", "title": "Export Transcriptome as FASTA", "topics": [ "exportFASTA" ] }, { "page": "exportGTF", "title": "Export GTF", "topics": [ "exportGTF" ] }, { "page": "exportMergeTable", "title": "Export Merge Table for Transcriptome", "topics": [ "exportMergeTable" ] }, { "page": "generateMergeTable", "title": "Generate Merge Table", "topics": [ "generateMergeTable", "generateMergeTable,TxDb-method" ] }, { "page": "truncateTxome", "title": "Truncate Transcriptome", "topics": [ "truncateTxome", "truncateTxome,TxDb-method" ] }, { "page": "txdbToGRangesList", "title": "Convert TxDb object to GRangesList", "topics": [ "txdbToGRangesList" ] } ], "_readme": "https://github.com/bioc/txcutr/raw/HEAD/README.md", "_rundeps": [ "abind", "AnnotationDbi", "askpass", "BH", "Biobase", "BiocBaseUtils", "BiocFileCache", "BiocGenerics", "BiocIO", "BiocParallel", "biomaRt", "Biostrings", "bit", "bit64", "bitops", "blob", "cachem", "cigarillo", "cli", "codetools", "cpp11", "crayon", "curl", "DBI", "dbplyr", "DelayedArray", "dplyr", "fastmap", "filelock", "formatR", "futile.logger", "futile.options", "generics", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "glue", "hms", "httr", "httr2", "IRanges", "jsonlite", "KEGGREST", "lambda.r", "lattice", "lifecycle", "magrittr", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mime", "openssl", "pillar", "pkgconfig", "png", "prettyunits", "progress", "purrr", "R6", "rappdirs", "RCurl", "restfulr", "Rhtslib", "rjson", "rlang", "Rsamtools", "RSQLite", "rtracklayer", "S4Arrays", "S4Vectors", "Seqinfo", "snow", "SparseArray", "stringi", "stringr", "SummarizedExperiment", "sys", "tibble", "tidyr", "tidyselect", "txdbmaker", "UCSC.utils", "utf8", "vctrs", "withr", "XML", "xml2", "XVector", "yaml" ], "_vignettes": [ { "source": "intro.Rmd", "filename": "intro.html", "title": "Introduction to txcutr", "author": "Mervin M Fansler", "engine": "knitr::rmarkdown", "headings": [ "Basics", "Motivation", "Install txcutr", "Required Background", "Asking for Help", "Citing txcutr", "Quick Start to Using txcutr", "Starting from TxDb Objects", "Example TxDb", "Transcriptome Truncation", "Exporting a New Annotation", "Exporting Sequences", "Merge Table", "Notes on Usage", "Making TxDb Objects", "BiocParallel", "Alternative Cleavage and Polyadenylation", "Reproducibility", "Bibliography" ], "created": "2021-09-14 18:33:40", "modified": "2024-03-19 23:02:11", "commits": 4 } ], "_score": 5.6020599913279625, "_indexed": true, "_nocasepkg": "txcutr", "_universes": [ "bioc", "mfansler" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.19.0", "date": "2026-07-05T03:03:54.000Z", "distro": "resolute", "commit": "f77e877da0650ce6b75bbc781bfd2b5f7dcd892f", "fileid": "https://r2.ropensci.org/7e95755215fc408ebe74d9fb89d8567e40690d3cc15776d4a2be5b8529b9b019", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28727468502" }, { "r": "4.6.1", "os": "linux", "version": "1.19.0", "date": "2026-07-05T03:03:43.000Z", "distro": "resolute", "commit": "f77e877da0650ce6b75bbc781bfd2b5f7dcd892f", "fileid": "https://r2.ropensci.org/ed43c65139c33718234bd1436406078abab8a843f914b279899420324e91c9d7", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28727468502" }, { "r": "4.5.3", "os": "mac", "version": "1.19.0", "date": "2026-07-05T03:00:53.000Z", "commit": "f77e877da0650ce6b75bbc781bfd2b5f7dcd892f", "fileid": "https://r2.ropensci.org/f329257f8c02557eee45e62a46c01888a55382da2d7b20aaccd7f2239b885a32", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28727468502" }, { "r": "4.6.1", "os": "mac", "version": "1.19.0", "date": "2026-07-05T03:00:58.000Z", "commit": "f77e877da0650ce6b75bbc781bfd2b5f7dcd892f", "fileid": "https://r2.ropensci.org/ae3f1a59a8bf75fb584fa5773bbddbb112b7d4ab2baf0c4755e3ffa97f92d0c3", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28727468502" }, { "r": "4.6.0", "os": "wasm", "version": "1.19.0", "date": "2026-07-05T03:03:15.000Z", "commit": "f77e877da0650ce6b75bbc781bfd2b5f7dcd892f", "fileid": "https://r2.ropensci.org/2cf13cbe2db326befb2e88bc641707aede2471fdeee0c6a349b6ec3dd424a794", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28727468502" }, { "r": "4.7.0", "os": "win", "version": "1.19.0", "date": "2026-07-05T03:02:17.000Z", "commit": "f77e877da0650ce6b75bbc781bfd2b5f7dcd892f", "fileid": "https://r2.ropensci.org/3ac16125c308378dd039c13355fa0273adec46f9afca2f1764c1570b6e92cbf1", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28727468502" }, { "r": "4.5.3", "os": "win", "version": "1.19.0", "date": "2026-07-05T03:01:31.000Z", "commit": "f77e877da0650ce6b75bbc781bfd2b5f7dcd892f", "fileid": "https://r2.ropensci.org/eae8d0814520fd8ee9665acdb98874e53bc60f1331011248acfb61f416494fc6", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28727468502" }, { "r": "4.6.1", "os": "win", "version": "1.19.0", "date": "2026-07-05T03:01:44.000Z", "commit": "f77e877da0650ce6b75bbc781bfd2b5f7dcd892f", "fileid": "https://r2.ropensci.org/648da1013c4cfc0153d061d6259e39b8c08a6353a0cff04c51491cdf94378184", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28727468502" } ] }