{ "_id": "6a1aaae91d7bb097a09d4d79", "Package": "regsplice", "Version": "1.39.0", "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": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:44:36 UTC", "RemoteUrl": "https://github.com/bioc/regsplice", "RemoteRef": "HEAD", "RemoteSha": "be97a76629082ffe9f29e58a14c610462b5c4df3", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 06:58:39 UTC", "User": "root" }, "MD5sum": "5ab391abeb46a24d0b0509fc6f821e8f", "_user": "bioc", "_type": "src", "_file": "regsplice_1.39.0.tar.gz", "_fileid": "f520b7765baa8839d0e3382ad87ef8263f7198f5489fdbc460b1b3bf3e770f9e", "_filesize": 231066, "_sha256": "f520b7765baa8839d0e3382ad87ef8263f7198f5489fdbc460b1b3bf3e770f9e", "_created": "2026-05-30T06:58:39.000Z", "_published": "2026-05-30T09:16:25.772Z", "_jobs": [ { "job": 78631909106, "time": 179, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7306286777" }, { "job": 78631909100, "time": 347, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7306306986" }, { "job": 78631909097, "time": 312, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7306303049" }, { "job": 78631909102, "time": 197, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7307089140" }, { "job": 78631909109, "time": 165, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7307086184" }, { "job": 78631697774, "time": 237, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7306265243" }, { "job": 78631909107, "time": 119, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7306279337" }, { "job": 78631909113, "time": 234, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7306293422" }, { "job": 78631909114, "time": 214, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7306290916" }, { "job": 78631909112, "time": 389, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7306312688" } ], "_bioccheck": { "error": 0, "warning": 1, "note": 11 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26677406789", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/regsplice", "_commit": { "id": "be97a76629082ffe9f29e58a14c610462b5c4df3", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380276 }, "_maintainer": { "name": "Lukas M. Weber", "email": "lmweb012@gmail.com", "login": "lmweber", "description": "Assistant Professor, Department of Biostatistics, Boston University", "uuid": 8062417 }, "_distro": "noble", "_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": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 4 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.39.0", "bioc": "3.24" }, { "branch": "release", "version": "1.38.0", "bioc": "3.23" } ], "_topics": [ "immunooncology", "alternativesplicing", "differentialexpression", "differentialsplicing", "sequencing", "rnaseq", "microarray", "exonarray", "experimentaldesign", "software" ], "_stars": 3, "_contributors": [ { "user": "lmweber", "count": 178, "uuid": 8062417 }, { "user": "nturaga", "count": 14, "uuid": 2746443 }, { "user": "jwokaty", "count": 12, "uuid": 1744257 }, { "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", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 377, "source": "https://www.bioconductor.org/packages/stats/bioc/regsplice" }, "_devurl": "https://github.com/lmweber/regsplice", "_searchresults": 33, "_rbuild": "4.6.0", "_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/regsplice.html", "manual.pdf" ], "_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/HEAD/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": 5.7737864449811935, "_indexed": true, "_nocasepkg": "regsplice", "_universes": [ "bioc", "lmweber" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.39.0", "date": "2026-04-30T15:29:30.000Z", "distro": "noble", "commit": "be97a76629082ffe9f29e58a14c610462b5c4df3", "fileid": "0cb8a5645d0c5c4b4ddeba9c9783ec28817f285ba7f32f9dc16f9ec7f284a388", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173589941" }, { "r": "4.6.0", "os": "linux", "version": "1.39.0", "date": "2026-04-30T15:28:33.000Z", "distro": "noble", "commit": "be97a76629082ffe9f29e58a14c610462b5c4df3", "fileid": "0aae0cb79a136a6cdc89c5b5d65b328beb1b02d01079c041a7ad4ffcd0cadff7", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173589941" }, { "r": "4.5.3", "os": "mac", "version": "1.39.0", "date": "2026-04-30T16:38:42.000Z", "commit": "be97a76629082ffe9f29e58a14c610462b5c4df3", "fileid": "bdff0c8a60fab3b85cc7f16f62de4a95f7553c33ffa70b145b59f224851845a4", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173589941" }, { "r": "4.6.0", "os": "mac", "version": "1.39.0", "date": "2026-04-30T16:39:13.000Z", "commit": "be97a76629082ffe9f29e58a14c610462b5c4df3", "fileid": "3147b01e86b427d54aab8b1bb4f74decf4f25415d418be0fc1f8738c6347c528", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173589941" }, { "r": "4.7.0", "os": "win", "version": "1.39.0", "date": "2026-04-30T15:26:33.000Z", "commit": "be97a76629082ffe9f29e58a14c610462b5c4df3", "fileid": "51b4e1eb4a9d52e75e3e56079373538cca5827c6df1d5337a3d323d42b889598", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173589941" }, { "r": "4.5.3", "os": "win", "version": "1.39.0", "date": "2026-04-30T15:26:45.000Z", "commit": "be97a76629082ffe9f29e58a14c610462b5c4df3", "fileid": "4ea760ed59abb990798fb1b03dcc81d978dd7012f39d6b55479707a627539bf2", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173589941" }, { "r": "4.6.0", "os": "win", "version": "1.39.0", "date": "2026-04-30T15:26:33.000Z", "commit": "be97a76629082ffe9f29e58a14c610462b5c4df3", "fileid": "017da806729db0002f88fc49357b26ee5b6c3634ccd18ce974f5a11a72b8eb87", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173589941" }, { "r": "4.6.0", "os": "wasm", "version": "1.39.0", "date": "2026-05-22T21:05:17.000Z", "commit": "be97a76629082ffe9f29e58a14c610462b5c4df3", "fileid": "426e6aa69fa280e0fd2a888c6cdd4e9414440d64e55d6fc81948f473e5723e32", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173589941" } ] }