{ "_id": "6accb17aa14063b82c3a7fda", "Package": "regsplice", "Version": "1.38.1", "Title": "L1-regularization based methods for detection of differential\nsplicing", "Description": "Statistical methods for detection of differential splicing\n(differential exon usage) in RNA-seq and exon microarray data,\nusing L1-regularization (lasso) to improve power.", "Authors@R": "person(\"Lukas M.\", \"Weber\", email = \"lmweb012@gmail.com\", role = c(\"aut\", \"cre\"))", "Author": "Lukas M. Weber [aut, cre]", "Maintainer": "Lukas M. Weber ", "URL": "https://github.com/lmweber/regsplice", "BugReports": "https://github.com/lmweber/regsplice/issues", "License": "MIT + file LICENSE", "VignetteBuilder": "knitr", "RoxygenNote": "7.1.0", "biocViews": "ImmunoOncology, AlternativeSplicing, DifferentialExpression,\nDifferentialSplicing, Sequencing, RNASeq, Microarray,\nExonArray, ExperimentalDesign, Software", "Collate": "'class_RegspliceResults.R' 'class_RegspliceData.R' 'LRTests.R'\n'createDesignMatrix.R' 'filterLowCounts.R' 'filterZeros.R'\n'fitting_functions_multiple_genes.R'\n'fitting_functions_single_gene.R' 'helper_functions.R'\n'initializeResults.R' 'regsplice_wrapper.R'\n'runNormalization.R' 'runVoom.R' 'summaryTable.R'", "Config/pak/sysreqs": "zlib1g-dev", "Repository": "Bioconductor 3.23", "Date/Publication": "2026-07-14 16:19:42 UTC", "RemoteUrl": "https://github.com/bioc/regsplice", "RemoteRef": "RELEASE_3_23", "RemoteSha": "abdeda773363b685fe32e00c742a0525313ec19e", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-12 10:02:00 UTC", "User": "root" }, "_user": "bioc-release", "_type": "src", "_file": "regsplice_1.38.1.tar.gz", "_fileid": "https://r2.ropensci.org/4119bca73593f77c3804138629d2e27c0a15a22c7b663b218662ea8eaba3843d", "_filesize": 229892, "_sha256": "4119bca73593f77c3804138629d2e27c0a15a22c7b663b218662ea8eaba3843d", "_expires": "2027-01-20T10:07:52.000Z", "_created": "2026-10-12T10:02:00.000Z", "_published": "2026-10-12T10:07:54.322Z", "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38233319923", "_status": "success", "_host": "GitHub-Actions", "_bioccheck": { "error": 0, "warning": 1, "note": 11 }, "_upstream": "https://github.com/bioc/regsplice", "_commit": { "id": "abdeda773363b685fe32e00c742a0525313ec19e", "author": "Lukas Weber ", "committer": "Lukas Weber ", "message": "email and version\n", "time": 1784045982 }, "_maintainer": { "name": "Lukas M. Weber", "email": "weberlm3@gmail.com", "login": "lmweber", "description": "Assistant Professor, Department of Biostatistics, Boston University", "uuid": 8062417 }, "_distro": "resolute", "_jobs": [ { "job": 114759427668, "time": 153, "config": "bioc-checks", "r": "4.6.1", "check": "WARNING", "artifact": "11739966455" }, { "job": 114759427580, "time": 294, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "11740456010" }, { "job": 114759427636, "time": 277, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "11739179117" }, { "job": 114759427711, "time": 266, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "11740246586" }, { "job": 114759427758, "time": 234, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "11739852005" }, { "job": 114757934857, "time": 221, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11739612674" }, { "job": 114759427529, "time": 101, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11740046247" }, { "job": 114759427800, "time": 208, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "11740435781" }, { "job": 114759427675, "time": 273, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "11739204050" }, { "job": 114759427780, "time": 225, "config": "windows-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "11739702298" } ], "_registered": true, "_dependencies": [ { "package": "glmnet", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "limma", "role": "Imports" }, { "package": "edgeR", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "pbapply", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "testthat", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 4 }, { "week": "2026-18", "n": 1 }, { "week": "2026-29", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.39.1", "bioc": "3.24", "repository": "bioc" }, { "branch": "release", "version": "1.38.1", "bioc": "3.23", "repository": "bioc" } ], "_topics": [ "immunooncology", "alternativesplicing", "differentialexpression", "differentialsplicing", "sequencing", "rnaseq", "microarray", "exonarray", "experimentaldesign", "software" ], "_stars": 4, "_contributors": [ { "user": "lmweber", "count": 179, "uuid": 8062417 }, { "user": "jwokaty", "count": 16, "uuid": 1744257 }, { "user": "nturaga", "count": 14, "uuid": 2746443 }, { "user": "hpages", "count": 2, "uuid": 8810451 }, { "user": "vobencha", "count": 2, "uuid": 2466173 }, { "user": "kayla-morrell", "count": 1, "uuid": 32339524 }, { "user": "link-ny", "count": 1, "uuid": 4392950 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 476, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 508, "source": "https://www.bioconductor.org/packages/stats/bioc/regsplice" }, "_devurl": "https://github.com/lmweber/regsplice", "_searchresults": 16, "_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/regsplice.html", "LICENSE" ], "_homeurl": "https://github.com/lmweber/regsplice", "_realowner": "bioc", "_cranurl": false, "_exports": [ "assays", "colData", "countsData", "createDesignMatrix", "df_tests", "filterLowCounts", "filterZeros", "fitFullMultiple", "fitNullMultiple", "fitRegMultiple", "gene_IDs", "initializeResults", "LR_stats", "LRTests", "p_adj", "p_vals", "regsplice", "RegspliceData", "RegspliceResults", "rowData", "runNormalization", "runVoom", "summaryTable", "weightsData" ], "_help": [ { "page": "createDesignMatrix", "title": "Create design matrix.", "topics": [ "createDesignMatrix" ] }, { "page": "filterLowCounts", "title": "Filter low-count exons.", "topics": [ "filterLowCounts" ] }, { "page": "filterZeros", "title": "Filter zero-count exons.", "topics": [ "filterZeros" ] }, { "page": "fitRegMultiple", "title": "Fit models.", "topics": [ "fitFullMultiple", "fitNullMultiple", "fitRegMultiple" ] }, { "page": "initializeResults", "title": "Initialize RegspliceResults object.", "topics": [ "initializeResults" ] }, { "page": "LRTests", "title": "Calculate likelihood ratio tests.", "topics": [ "LRTests" ] }, { "page": "regsplice", "title": "Wrapper function to run regsplice.", "topics": [ "regsplice" ] }, { "page": "RegspliceData", "title": "RegspliceData objects.", "topics": [ "assays,RegspliceData-method", "colData,RegspliceData-method", "countsData", "countsData,RegspliceData-method", "RegspliceData", "RegspliceData-class", "rowData,RegspliceData-method", "weightsData", "weightsData,RegspliceData-method", "[,RegspliceData,ANY,ANY,ANY-method" ] }, { "page": "RegspliceResults", "title": "RegspliceResults objects.", "topics": [ "df_tests", "df_tests,RegspliceResults-method", "gene_IDs", "gene_IDs,RegspliceResults-method", "LR_stats", "LR_stats,RegspliceResults-method", "p_adj", "p_adj,RegspliceResults-method", "p_vals", "p_vals,RegspliceResults-method", "RegspliceResults", "RegspliceResults-class" ] }, { "page": "runNormalization", "title": "Calculate normalization factors.", "topics": [ "runNormalization" ] }, { "page": "runVoom", "title": "Calculate 'voom' transformation and weights.", "topics": [ "runVoom" ] }, { "page": "summaryTable", "title": "Summary table.", "topics": [ "summaryTable" ] } ], "_readme": "https://github.com/bioc/regsplice/raw/RELEASE_3_23/README.md", "_rundeps": [ "abind", "Biobase", "BiocGenerics", "codetools", "DelayedArray", "edgeR", "foreach", "generics", "GenomicRanges", "glmnet", "IRanges", "iterators", "lattice", "limma", "locfit", "Matrix", "MatrixGenerics", "matrixStats", "pbapply", "Rcpp", "RcppEigen", "S4Arrays", "S4Vectors", "Seqinfo", "shape", "SparseArray", "statmod", "SummarizedExperiment", "survival", "XVector" ], "_vignettes": [ { "source": "regsplice-workflow.Rmd", "filename": "regsplice-workflow.html", "title": "regsplice workflow", "author": "Lukas M. Weber, Mark D. Robinson", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Example workflow", "Data set", "Exon microarray data", "Workflow", "Load data and create condition vector", "Run workflow with wrapper function", "Summary table of results", "Run workflow using functions for individual steps", "Create RegspliceData object", "Filter zero-count exon bins", "Filter low-count exons", "Calculate normalization factors", "'voom' transformation and weights", "Initialize RegspliceResults object", "Fit models", "Calculate likelihood ratio tests", "Analyze results", "Summary of all significant genes", "Contingency table", "Additional information", "Additional user options", "Design matrices" ], "created": "2016-10-15 14:12:13", "modified": "2019-11-28 19:59:11", "commits": 51 } ], "_score": 5.760422483423213, "_indexed": false, "_nocasepkg": "regsplice", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/regsplice", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.38.1", "date": "2026-10-12T10:05:28.000Z", "distro": "resolute", "commit": "abdeda773363b685fe32e00c742a0525313ec19e", "fileid": "https://r2.ropensci.org/7686539c3289d47a2bd80152b595d9944cb227b454888d48fb6374de14d7dec4", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38233319923" }, { "r": "4.6.1", "os": "linux", "version": "1.38.1", "date": "2026-10-12T10:05:29.000Z", "distro": "resolute", "commit": "abdeda773363b685fe32e00c742a0525313ec19e", "fileid": "https://r2.ropensci.org/78f17608e5563bc7a03a8ecb99f3dd25dfeff60e042bc6319557dc384a0da9f7", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38233319923" }, { "r": "4.5.3", "os": "mac", "version": "1.38.1", "date": "2026-10-12T10:04:15.000Z", "commit": "abdeda773363b685fe32e00c742a0525313ec19e", "fileid": "https://r2.ropensci.org/bab91bf2b0ee9662629a4bf2d4b55ac841295c86c79105357e5d8c0f12be601d", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38233319923" }, { "r": "4.6.1", "os": "mac", "version": "1.38.1", "date": "2026-10-12T10:04:10.000Z", "commit": "abdeda773363b685fe32e00c742a0525313ec19e", "fileid": "https://r2.ropensci.org/87ad6489fe5e7b8366a248830497e503aa5559731ce1fb58a200c1c0c1c0b4be", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38233319923" }, { "r": "4.6.0", "os": "wasm", "version": "1.38.1", "date": "2026-10-12T10:04:17.000Z", "commit": "abdeda773363b685fe32e00c742a0525313ec19e", "fileid": "https://r2.ropensci.org/a8f2b04d14c0b510405b75afae0c43c1227a79d83b1f175f8b18653f72bd5bab", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38233319923" }, { "r": "4.7.0", "os": "win", "version": "1.38.1", "date": "2026-10-12T10:03:48.000Z", "commit": "abdeda773363b685fe32e00c742a0525313ec19e", "fileid": "https://r2.ropensci.org/fd9bbab772ae62299a0d5019f87302790244221287fbc16630691123acc54eca", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38233319923" }, { "r": "4.5.3", "os": "win", "version": "1.38.1", "date": "2026-10-12T10:03:31.000Z", "commit": "abdeda773363b685fe32e00c742a0525313ec19e", "fileid": "https://r2.ropensci.org/cda0c8eb06af2dee0de3542ada1c64e71a4a675172336b1c51728edefc520e80", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38233319923" }, { "r": "4.6.1", "os": "win", "version": "1.38.1", "date": "2026-10-12T10:03:40.000Z", "commit": "abdeda773363b685fe32e00c742a0525313ec19e", "fileid": "https://r2.ropensci.org/0938042e115b00fa60072b3b6ede67ec6b9ae707d1ea397ef2553aac8f512415", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38233319923" } ] }