{ "_id": "6a49f64d8408e3d40c0b3e23", "Package": "diffUTR", "Type": "Package", "Title": "diffUTR: Streamlining differential exon and 3' UTR usage", "Version": "1.21.0", "Authors@R": "c(\nperson(\"Pierre-Luc\", \"Germain\", email=\"pierre-luc.germain@hest.ethz.ch\",\nrole=c(\"cre\",\"aut\"), comment = c(ORCID = \"0000-0003-3418-4218\")),\nperson(\"Stefan\", \"Gerber\", email=\"gerberst@student.ethz.ch\", role=\"aut\") )", "Description": "The diffUTR package provides a uniform interface and\nplotting functions for limma/edgeR/DEXSeq -powered differential\nbin/exon usage. It includes in addition an improved version of\nthe limma::diffSplice method. Most importantly, diffUTR further\nextends the application of these frameworks to differential UTR\nusage analysis using poly-A site databases.", "biocViews": "GeneExpression", "BugReports": "https://github.com/ETHZ-INS/diffUTR", "VignetteBuilder": "knitr", "License": "GPL-3", "Encoding": "UTF-8", "RoxygenNote": "7.1.2", "Config/pak/sysreqs": "make libbz2-dev libicu-dev liblzma-dev libpng-dev\nlibxml2-dev libssl-dev perl xz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:56:02 UTC", "RemoteUrl": "https://github.com/bioc/diffUTR", "RemoteRef": "HEAD", "RemoteSha": "412a54c5cd368418d298426fb7b6d4dbb37d4423", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-12 06:42:29 UTC", "User": "root" }, "Author": "Pierre-Luc Germain [cre, aut] (ORCID:\n),\nStefan Gerber [aut]", "Maintainer": "Pierre-Luc Germain ", "_user": "bioc", "_type": "src", "_file": "diffUTR_1.21.0.tar.gz", "_fileid": "https://r2.ropensci.org/3b492e0fab0c8b316c5cc01990030561e4d88c1e7fb6616809fcfbff2f6a5e8d", "_filesize": 1118640, "_sha256": "3b492e0fab0c8b316c5cc01990030561e4d88c1e7fb6616809fcfbff2f6a5e8d", "_expires": "2026-10-13T06:14:35.000Z", "_created": "2026-06-12T06:42:29.000Z", "_published": "2026-07-05T06:14:37.677Z", "_bioccheck": { "error": 0, "warning": 0, "note": 11 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/27399211067", "_status": "success", "_upstream": "https://github.com/bioc/diffUTR", "_commit": { "id": "412a54c5cd368418d298426fb7b6d4dbb37d4423", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380962 }, "_maintainer": { "name": "Pierre-Luc Germain", "email": "pierre-luc.germain@hest.ethz.ch", "login": "plger", "orcid": "0000-0003-3418-4218", "description": "like sailors who on the open sea must reconstruct their ship but are never able to start afresh from the bottom...", "uuid": 9786697 }, "_distro": "noble", "_jobs": [ { "job": 85198392132, "time": 221, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7584909751" }, { "job": 85198392201, "time": 470, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7584976678" }, { "job": 85198392289, "time": 383, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7584953289" }, { "job": 85198392240, "time": 287, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7584926913" }, { "job": 85198392134, "time": 348, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7584943098" }, { "job": 85198392033, "time": 322, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7584850025" }, { "job": 85198392095, "time": 177, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7584898211" }, { "job": 85198392258, "time": 330, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7584938415" }, { "job": 85198392254, "time": 324, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7584936924" }, { "job": 85198392239, "time": 353, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7584944545" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0", "role": "Depends" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "limma", "role": "Imports" }, { "package": "edgeR", "role": "Imports" }, { "package": "DEXSeq", "role": "Imports" }, { "package": "GenomicRanges", "role": "Imports" }, { "package": "Rsubread", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "rtracklayer", "role": "Imports" }, { "package": "ComplexHeatmap", "role": "Imports" }, { "package": "ggrepel", "role": "Imports" }, { "package": "stringi", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "GenomeInfoDb", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "matrixStats", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "ensembldb", "role": "Imports" }, { "package": "viridisLite", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.21.0", "bioc": "3.24" }, { "branch": "release", "version": "1.20.0", "bioc": "3.23" } ], "_topics": [ "geneexpression" ], "_stars": 7, "_contributors": [ { "user": "plger", "count": 121, "uuid": 9786697 }, { "user": "jwokaty", "count": 10, "uuid": 1744257 }, { "user": "nturaga", "count": 6, "uuid": 2746443 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 334, "source": "https://www.bioconductor.org/packages/stats/bioc/diffUTR" }, "_mentions": 1, "_devurl": "https://github.com/ethz-ins/diffutr", "_searchresults": 11, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/diffUTR.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/ethz-ins/diffutr", "_realowner": "bioc", "_cranurl": false, "_exports": [ "addNormalizedAssays", "countFeatures", "deuBinPlot", "DEXSeqWrapper", "diffSplice2", "diffSpliceDGEWrapper", "diffSpliceWrapper", "geneBinHeatmap", "geneLevelStats", "plotTopGenes", "prepareBins", "simesAggregation" ], "_datasets": [ { "name": "example_bin_se", "title": "Example bin-level 'RangedSummarizedExperiment'", "object": "example_bin_se", "file": "example_bin_se.RData", "class": [ "RangedSummarizedExperiment" ], "fields": [], "table": false, "tojson": false }, { "name": "example_gene_annotation", "title": "Example gene annotation", "object": "example_gene_annotation", "file": "example_gene_annotation.RData", "class": [ "GRanges" ], "fields": [], "table": false, "tojson": false }, { "name": "rn6_PAS", "title": "Poly-A sites compendium for Rattus Norvegicus (Rno6)", "object": "rn6_PAS", "file": "rn6_PAS.RData", "class": [ "GRanges" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "addNormalizedAssays", "title": "addNormalizedAssays", "topics": [ "addNormalizedAssays" ] }, { "page": "countFeatures", "title": "countFeatures", "topics": [ "countFeatures" ] }, { "page": "deuBinPlot", "title": "deuBinPlot", "topics": [ "deuBinPlot" ] }, { "page": "diffSplice2", "title": "diffSplice2", "topics": [ "diffSplice2" ] }, { "page": "DEUwrappers", "title": "DEUwrappers", "topics": [ "DEUwrappers", "DEXSeqWrapper", "diffSpliceDGEWrapper", "diffSpliceWrapper" ] }, { "page": "example_bin_se", "title": "Example bin-level `RangedSummarizedExperiment`", "topics": [ "example_bin_se" ] }, { "page": "example_gene_annotation", "title": "Example gene annotation", "topics": [ "example_gene_annotation" ] }, { "page": "geneBinHeatmap", "title": "geneBinHeatmap", "topics": [ "geneBinHeatmap" ] }, { "page": "geneLevelStats", "title": "geneLevelStats", "topics": [ "geneLevelStats" ] }, { "page": "plotTopGenes", "title": "plotTopGenes", "topics": [ "plotTopGenes" ] }, { "page": "prepareBins", "title": "prepareBins", "topics": [ "prepareBins" ] }, { "page": "rn6_PAS", "title": "Poly-A sites compendium for Rattus Norvegicus (Rno6)", "topics": [ "rn6_PAS" ] }, { "page": "simesAggregation", "title": "simesAggregation", "topics": [ "simesAggregation" ] } ], "_readme": "https://github.com/bioc/diffUTR/raw/HEAD/README.md", "_rundeps": [ "abind", "annotate", "AnnotationDbi", "AnnotationFilter", "askpass", "BH", "Biobase", "BiocBaseUtils", "BiocFileCache", "BiocGenerics", "BiocIO", "BiocParallel", "biomaRt", "Biostrings", "bit", "bit64", "bitops", "blob", "cachem", "cigarillo", "circlize", "cli", "clue", "cluster", "codetools", "colorspace", "ComplexHeatmap", "cpp11", "crayon", "curl", "DBI", "dbplyr", "DelayedArray", "DESeq2", "DEXSeq", "digest", "doParallel", "dplyr", "edgeR", "ensembldb", "farver", "fastmap", "filelock", "foreach", "formatR", "futile.logger", "futile.options", "genefilter", "geneplotter", "generics", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "GetoptLong", "ggplot2", "ggrepel", "GlobalOptions", "glue", "gtable", "hms", "httr", "httr2", "hwriter", "IRanges", "isoband", "iterators", "jsonlite", "KEGGREST", "labeling", "lambda.r", "lattice", "lazyeval", "lifecycle", "limma", "locfit", "magrittr", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mime", "openssl", "pillar", "pkgconfig", "png", "prettyunits", "progress", "ProtGenerics", "purrr", "R6", "rappdirs", "RColorBrewer", "Rcpp", "RcppArmadillo", "RCurl", "restfulr", "Rhtslib", "rjson", "rlang", "Rsamtools", "RSQLite", "Rsubread", "rtracklayer", "S4Arrays", "S4Vectors", "S7", "scales", "Seqinfo", "shape", "snow", "SparseArray", "statmod", "stringi", "stringr", "SummarizedExperiment", "survival", "sys", "tibble", "tidyr", "tidyselect", "UCSC.utils", "utf8", "vctrs", "viridisLite", "withr", "XML", "xml2", "xtable", "XVector", "yaml" ], "_vignettes": [ { "source": "diffUTR.Rmd", "filename": "diffUTR.html", "title": "diffUTR", "author": "Pierre-Luc Germain", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Differential exon usage", "Differential 3' UTR usage", "Getting started", "Package installation", "Obtaining gene annotations", "Workflow for differential exon usage (DEU) analysis", "Preparing the annotation", "Counting reads in bins", "Differential analysis", "Workflow for differential 3' UTR usage analysis", "Obtaining alternative poly-adenlyation sites and preparing the bins", "Counting and differential analysis:", "Exploring the results", "Top genes", "Gene profiles", "Overlaying with transcripts" ], "created": "2021-02-04 19:23:33", "modified": "2021-05-03 19:36:29", "commits": 8 }, { "source": "diffSplice2.Rmd", "filename": "diffSplice2.html", "title": "diffUTR - diffSplice2", "author": "Stefan Gerber, Pierre-Luc Germain", "engine": "knitr::rmarkdown", "headings": [], "created": "2021-05-03 19:03:27", "modified": "2021-05-03 19:03:27", "commits": 1 } ], "_score": 5.488550716500445, "_indexed": true, "_nocasepkg": "diffutr", "_universes": [ "bioc", "plger", "ethz-ins" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.21.0", "date": "2026-06-12T06:46:50.000Z", "distro": "noble", "commit": "412a54c5cd368418d298426fb7b6d4dbb37d4423", "fileid": "https://r2.ropensci.org/4b5eeb53337384830fb6ef462c28928b94ac1608378f1f18a4c6eb525520747f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27399211067" }, { "r": "4.6.0", "os": "linux", "version": "1.21.0", "date": "2026-06-12T06:45:57.000Z", "distro": "noble", "commit": "412a54c5cd368418d298426fb7b6d4dbb37d4423", "fileid": "https://r2.ropensci.org/3ebd9317ea891a1daca521e0f5294ad579cb145554fc6852a0cf60484bc132e8", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27399211067" }, { "r": "4.5.3", "os": "mac", "version": "1.21.0", "date": "2026-06-12T06:44:57.000Z", "commit": "412a54c5cd368418d298426fb7b6d4dbb37d4423", "fileid": "https://r2.ropensci.org/9c4b3d03f9838ef974613ed4b2718f4c49dafb1807a47af10ef2482fd58e95e6", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27399211067" }, { "r": "4.6.0", "os": "mac", "version": "1.21.0", "date": "2026-06-12T06:45:13.000Z", "commit": "412a54c5cd368418d298426fb7b6d4dbb37d4423", "fileid": "https://r2.ropensci.org/ac211703cc4f1319766ac0b59b8dbebcb056f8d6c32796c6397fa6afa3eea81c", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27399211067" }, { "r": "4.6.0", "os": "wasm", "version": "1.21.0", "date": "2026-06-12T06:46:08.000Z", "commit": "412a54c5cd368418d298426fb7b6d4dbb37d4423", "fileid": "https://r2.ropensci.org/acedee3be374000b2f5b537ffb9e85b778fbac24ad7c39d8163a7dccb2a0443a", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27399211067" }, { "r": "4.7.0", "os": "win", "version": "1.21.0", "date": "2026-06-12T06:44:42.000Z", "commit": "412a54c5cd368418d298426fb7b6d4dbb37d4423", "fileid": "https://r2.ropensci.org/0eb74f38442c3c54551dd9a421230b7b9e757e553286e9b5482cac2037882f89", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27399211067" }, { "r": "4.5.3", "os": "win", "version": "1.21.0", "date": "2026-06-12T06:44:35.000Z", "commit": "412a54c5cd368418d298426fb7b6d4dbb37d4423", "fileid": "https://r2.ropensci.org/cf2069c9df1ec251ef5dd8378abd6f623c41598ffd6deb0100cb6b3df1e8bd31", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27399211067" }, { "r": "4.6.0", "os": "win", "version": "1.21.0", "date": "2026-06-12T06:45:08.000Z", "commit": "412a54c5cd368418d298426fb7b6d4dbb37d4423", "fileid": "https://r2.ropensci.org/7e5c55d6859c5cbef7caf4e4c9095100309ac6185cc6abb2f319a444f924b3d7", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27399211067" } ] }