{ "_id": "6a4958eaf6c47c441949d8f3", "Package": "LRDE", "Type": "Package", "Title": "Differential Expression Analysis with Long Read RNA-Seq Data", "Version": "1.1.1", "Authors@R": "c(\nperson(given = \"Ziyang\", family = \"Liu\", email = \"jacobleo773@gmail.com\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0009-0004-2098-434X\")),\nperson(given = \"Hongxu\", family = \"Ding\", email = \"hongxuding@arizona.edu\", role = c(\"aut\", \"fnd\")),\nperson(given = \"Xiaoxiao\", family = \"Sun\", email = \"xiaosun@arizona.edu\", role = c(\"aut\", \"fnd\")),\nperson(given = \"Ziyuan\", family = \"Wang\", email = \"princezwang@arizona.edu\", role = c(\"aut\", \"fnd\"))\n)", "Description": "Provides hurdle negative binomial models for differential\nexpression analysis with long-read RNA-Seq data.", "biocViews": "Software, DifferentialExpression, Sequencing, RNASeq,\nLongRead, GeneExpression, Regression", "URL": "https://github.com/ziyang773/LRDE", "BugReports": "https://github.com/ziyang773/LRDE/issues", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Config/pak/sysreqs": "zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-06-25 16:26:40 UTC", "RemoteUrl": "https://github.com/bioc/LRDE", "RemoteRef": "HEAD", "RemoteSha": "e2383aa99cc5b8ec128e5c465696631794e4c0b8", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-25 21:34:23 UTC", "User": "root" }, "Author": "Ziyang Liu [aut, cre] (ORCID: ),\nHongxu Ding [aut, fnd],\nXiaoxiao Sun [aut, fnd],\nZiyuan Wang [aut, fnd]", "Maintainer": "Ziyang Liu ", "_user": "bioc", "_type": "src", "_file": "LRDE_1.1.1.tar.gz", "_fileid": "https://r2.ropensci.org/abfd196bb015ece5e5650ab2b1c4edc12ab776e9a229e86ed252f771a94b3602", "_filesize": 154805, "_sha256": "abfd196bb015ece5e5650ab2b1c4edc12ab776e9a229e86ed252f771a94b3602", "_expires": "2026-10-12T19:03:04.000Z", "_created": "2026-06-25T21:34:23.000Z", "_published": "2026-07-04T19:03:06.380Z", "_bioccheck": { "error": 0, "warning": 0, "note": 6 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28201785069", "_status": "success", "_upstream": "https://github.com/bioc/LRDE", "_commit": { "id": "e2383aa99cc5b8ec128e5c465696631794e4c0b8", "author": "Ziyang Liu ", "committer": "Ziyang Liu ", "message": "Update NEWS\n", "time": 1782404800 }, "_maintainer": { "name": "Ziyang Liu", "email": "jacobleo773@gmail.com", "login": "ziyang773", "description": "", "uuid": 61805413 }, "_distro": "resolute", "_jobs": [ { "job": 85158819218, "time": 213, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7891538720" }, { "job": 85158819172, "time": 309, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7891571030" }, { "job": 85158819089, "time": 237, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7891546515" }, { "job": 85158819181, "time": 148, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7891516958" }, { "job": 85158819082, "time": 210, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7891537671" }, { "job": 85158818921, "time": 196, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7891465479" }, { "job": 85158819058, "time": 128, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7891510043" }, { "job": 85158819233, "time": 176, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7891526922" }, { "job": 85158819340, "time": 174, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7891525422" }, { "job": 85158819095, "time": 175, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7891526028" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.5.0", "role": "Depends" }, { "package": "stats", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "BiocGenerics", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-12", "n": 11 }, { "week": "2026-14", "n": 4 }, { "week": "2026-15", "n": 6 }, { "week": "2026-16", "n": 1 }, { "week": "2026-18", "n": 2 }, { "week": "2026-26", "n": 3 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.1.0", "bioc": "3.24" }, { "branch": "release", "version": "0.99.6", "bioc": "3.23" } ], "_topics": [ "software", "differentialexpression", "sequencing", "rnaseq", "longread", "geneexpression", "regression" ], "_stars": 0, "_contributors": [ { "user": "ziyang773", "count": 25, "uuid": 61805413 }, { "user": "jwokaty", "count": 2, "uuid": 1744257 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 441, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_devurl": "https://github.com/ziyang773/lrde", "_searchresults": 4, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/LRDE.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "LICENSE", "manual.pdf" ], "_homeurl": "https://github.com/ziyang773/lrde", "_realowner": "bioc", "_cranurl": false, "_exports": [ "hurdle_LRT.dist", "hurdle_LRT.mean", "hurdle_Wald_Test.dist", "hurdle_Wald_Test.mean", "hurdle.LRT", "hurdle.Wald.Test", "prepareDGE", "sizeFactorsEst", "tagwiseEst" ], "_help": [ { "page": "LRDE-package", "title": "LRDE: Differential Expression Analysis for Long-Read RNA-Seq Data", "topics": [ "LRDE-package", "LRDE" ] }, { "page": "hurdle_LRT.dist", "title": "Distributional Likelihood Ratio Test for Hurdle Negative Binomial Model", "topics": [ "hurdle_LRT.dist" ] }, { "page": "hurdle_LRT.mean", "title": "Mean-Based Likelihood Ratio Test for Hurdle Negative Binomial Model", "topics": [ "hurdle_LRT.mean" ] }, { "page": "hurdle_Wald_Test.dist", "title": "Distributional Wald Test for Hurdle Negative Binomial Model", "topics": [ "hurdle_Wald_Test.dist" ] }, { "page": "hurdle_Wald_Test.mean", "title": "Mean-Based Wald Test for Hurdle Negative Binomial Model", "topics": [ "hurdle_Wald_Test.mean" ] }, { "page": "hurdle.LRT", "title": "Likelihood Ratio Test for Hurdle Negative Binomial Model", "topics": [ "hurdle.LRT" ] }, { "page": "hurdle.Wald.Test", "title": "Wald Test for Hurdle Negative Binomial Model", "topics": [ "hurdle.Wald.Test" ] }, { "page": "prepareDGE", "title": "Prepare Count Data for Differential Expression Analysis", "topics": [ "prepareDGE" ] }, { "page": "sizeFactorsEst", "title": "Estimate Size Factors for Normalization", "topics": [ "sizeFactorsEst" ] }, { "page": "tagwiseEst", "title": "Tag-wise Dispersion Estimation for Hurdle Negative Binomial Model", "topics": [ "tagwiseEst" ] } ], "_readme": "https://github.com/bioc/LRDE/raw/HEAD/README.md", "_rundeps": [ "abind", "Biobase", "BiocGenerics", "DelayedArray", "generics", "GenomicRanges", "IRanges", "lattice", "Matrix", "MatrixGenerics", "matrixStats", "S4Arrays", "S4Vectors", "Seqinfo", "SparseArray", "SummarizedExperiment", "XVector" ], "_vignettes": [ { "source": "LRDE-vignette.Rmd", "filename": "LRDE-vignette.html", "title": "Differential Expression Analysis with Long Read RNA-Seq Data", "author": "Ziyang Liu, Hongxu Ding", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Statistical Methodology", "1. Hurdle Model", "2. Information Borrowing via Empirical Bayes", "3. Differential Expression Testing", "Data Structure", "Example Workflow", "Interpreting Results", "Multiple Testing Correction", "Supported Input Format", "Session Information" ], "created": "2026-03-19 17:56:05", "modified": "2026-06-24 23:58:29", "commits": 4 } ], "_score": 4.477121254719663, "_indexed": true, "_nocasepkg": "lrde", "_universes": [ "bioc", "ziyang773" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.1.1", "date": "2026-06-25T21:38:11.000Z", "distro": "resolute", "commit": "e2383aa99cc5b8ec128e5c465696631794e4c0b8", "fileid": "https://r2.ropensci.org/5f4446877bb9bdd30d1975a5e663adbb14434cda228179219b8d97f684a06814", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28201785069" }, { "r": "4.6.0", "os": "linux", "version": "1.1.1", "date": "2026-06-25T21:37:13.000Z", "distro": "resolute", "commit": "e2383aa99cc5b8ec128e5c465696631794e4c0b8", "fileid": "https://r2.ropensci.org/bd8dba1149de4d4d15c9d8fa2f1d53ce194d2fc63daa92ebd8903e7bc6da8c10", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28201785069" }, { "r": "4.5.3", "os": "mac", "version": "1.1.1", "date": "2026-06-25T21:36:09.000Z", "commit": "e2383aa99cc5b8ec128e5c465696631794e4c0b8", "fileid": "https://r2.ropensci.org/4d342510a2f41ba2750ca614ddcad79c4dd7968b3346df17bbc46b0c24ac0436", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28201785069" }, { "r": "4.6.0", "os": "mac", "version": "1.1.1", "date": "2026-06-25T21:36:26.000Z", "commit": "e2383aa99cc5b8ec128e5c465696631794e4c0b8", "fileid": "https://r2.ropensci.org/31b892da626f9e9a6680fd90269cee2065955005d973ceb57fe3cb4278e228d6", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28201785069" }, { "r": "4.6.0", "os": "wasm", "version": "1.1.1", "date": "2026-06-25T21:36:57.000Z", "commit": "e2383aa99cc5b8ec128e5c465696631794e4c0b8", "fileid": "https://r2.ropensci.org/f82bc5ca3b9df0c16586114fa443fd76369a9966dd2d85e61fe3283fcf5c6503", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28201785069" }, { "r": "4.7.0", "os": "win", "version": "1.1.1", "date": "2026-06-25T21:35:54.000Z", "commit": "e2383aa99cc5b8ec128e5c465696631794e4c0b8", "fileid": "https://r2.ropensci.org/282519e0e64546b40bc0460cc105c555dff515076092a82294c8cc7a590438cb", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28201785069" }, { "r": "4.5.3", "os": "win", "version": "1.1.1", "date": "2026-06-25T21:35:52.000Z", "commit": "e2383aa99cc5b8ec128e5c465696631794e4c0b8", "fileid": "https://r2.ropensci.org/f8336f565c200d4fbdfcd8d5050928735c4a3694138b127ad6237fee3724d601", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28201785069" }, { "r": "4.6.0", "os": "win", "version": "1.1.1", "date": "2026-06-25T21:35:55.000Z", "commit": "e2383aa99cc5b8ec128e5c465696631794e4c0b8", "fileid": "https://r2.ropensci.org/a2858b30f1e81d0221491f2305555008d21841069d76349792b3f959ef6054c8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28201785069" } ] }