{ "_id": "6a5c681b9baadeef8ab4f950", "Package": "eisaR", "Title": "Exon-Intron Split Analysis (EISA) in R", "Version": "1.25.0", "Authors@R": "c(person(\"Michael\", \"Stadler\", email = \"michael.stadler@fmi.ch\", role = c(\"aut\", \"cre\")),\nperson(\"Dimos\", \"Gaidatzis\", email = \"dimosthenis.gaidatzis@fmi.ch\", role = \"aut\"),\nperson(\"Lukas\", \"Burger\", email = \"lukas.burger@fmi.ch\", role = \"aut\"),\nperson(\"Charlotte\", \"Soneson\", email = \"charlotte.soneson@fmi.ch\", role = \"aut\"))", "Description": "Exon-intron split analysis (EISA) uses ordinary RNA-seq\ndata to measure changes in mature RNA and pre-mRNA reads across\ndifferent experimental conditions to quantify transcriptional\nand post-transcriptional regulation of gene expression. For\ndetails see Gaidatzis et al., Nat Biotechnol 2015. doi:\n10.1038/nbt.3269. eisaR implements the major steps of EISA in\nR.", "License": "GPL-3", "biocViews": "Transcription, GeneExpression, GeneRegulation,\nFunctionalGenomics, Transcriptomics, Regression, RNASeq", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.1", "VignetteBuilder": "knitr", "URL": "https://github.com/fmicompbio/eisaR", "BugReports": "https://github.com/fmicompbio/eisaR/issues", "Config/pak/sysreqs": "zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:52:05 UTC", "RemoteUrl": "https://github.com/bioc/eisaR", "RemoteRef": "HEAD", "RemoteSha": "939131c9258887133e733741652c681a45e71d1a", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-19 05:52:31 UTC", "User": "root" }, "Author": "Michael Stadler [aut, cre],\nDimos Gaidatzis [aut],\nLukas Burger [aut],\nCharlotte Soneson [aut]", "Maintainer": "Michael Stadler ", "_user": "bioc", "_type": "src", "_file": "eisaR_1.25.0.tar.gz", "_fileid": "https://r2.ropensci.org/6edc0aab58f15159ff3186d19a35ffd407bbf05242078e99c0d6aa94f5c0975d", "_filesize": 1498757, "_sha256": "6edc0aab58f15159ff3186d19a35ffd407bbf05242078e99c0d6aa94f5c0975d", "_expires": "2026-10-27T06:00:57.000Z", "_created": "2026-07-19T05:52:31.000Z", "_published": "2026-07-19T06:00:59.096Z", "_bioccheck": { "error": 0, "warning": 1, "note": 8 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/29675371280", "_status": "success", "_upstream": "https://github.com/bioc/eisaR", "_commit": { "id": "939131c9258887133e733741652c681a45e71d1a", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380725 }, "_maintainer": { "name": "Michael Stadler", "email": "michael.stadler@fmi.ch", "login": "mbstadler", "description": "", "uuid": 13657342 }, "_distro": "resolute", "_jobs": [ { "job": 88162181743, "time": 258, "config": "bioc-checks", "r": "4.6.1", "check": "WARNING", "artifact": "8438770656" }, { "job": 88162181771, "time": 450, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "8438799122" }, { "job": 88162181765, "time": 387, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "8438789420" }, { "job": 88162181762, "time": 227, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "8438766415" }, { "job": 88162181769, "time": 238, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "8438767803" }, { "job": 88161770619, "time": 363, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8438734886" }, { "job": 88162181747, "time": 218, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8438765208" }, { "job": 88162181761, "time": 328, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "8438780753" }, { "job": 88162181749, "time": 307, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "8438777602" }, { "job": 88162181760, "time": 357, "config": "windows-release", "r": "4.6.1", "check": "NOTE", "artifact": "8438784693" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1", "role": "Depends" }, { "package": "graphics", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "GenomicRanges", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "limma", "role": "Imports" }, { "package": "edgeR", "version": ">= 4.0", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "BiocGenerics", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "QuasR", "role": "Suggests" }, { "package": "Rbowtie", "role": "Suggests" }, { "package": "Rhisat2", "role": "Suggests" }, { "package": "Biostrings", "role": "Suggests" }, { "package": "BSgenome", "role": "Suggests" }, { "package": "BSgenome.Hsapiens.UCSC.hg38", "role": "Suggests" }, { "package": "ensembldb", "role": "Suggests" }, { "package": "AnnotationDbi", "role": "Suggests" }, { "package": "GenomicFeatures", "role": "Suggests" }, { "package": "txdbmaker", "role": "Suggests" }, { "package": "rtracklayer", "role": "Suggests" }, { "package": "withr", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-37", "n": 1 }, { "week": "2025-44", "n": 2 }, { "week": "2025-45", "n": 1 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.25.0", "bioc": "3.24" }, { "branch": "release", "version": "1.24.0", "bioc": "3.23" } ], "_topics": [ "transcription", "geneexpression", "generegulation", "functionalgenomics", "transcriptomics", "regression", "rnaseq" ], "_stars": 17, "_contributors": [ { "user": "mbstadler", "count": 147, "uuid": 13657342 }, { "user": "csoneson", "count": 83, "uuid": 5628952 }, { "user": "jwokaty", "count": 16, "uuid": 1744257 }, { "user": "nturaga", "count": 10, "uuid": 2746443 }, { "user": "federicomarini", "count": 1, "uuid": 7447478 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 449, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 496, "source": "https://www.bioconductor.org/packages/stats/bioc/eisaR" }, "_mentions": 1, "_devurl": "https://github.com/fmicompbio/eisar", "_searchresults": 82, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/eisaR.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/fmicompbio/eisar", "_realowner": "bioc", "_cranurl": false, "_exports": [ "exportToGtf", "getFeatureRanges", "getRegionsFromTxDb", "getTx2Gene", "plotEISA", "runEISA" ], "_help": [ { "page": "exportToGtf", "title": "Export GRangesList to GTF", "topics": [ "exportToGtf" ] }, { "page": "getFeatureRanges", "title": "Generate a GRangesList object with feature ranges", "topics": [ "getFeatureRanges" ] }, { "page": "getRegionsFromTxDb", "title": "Get exonic/gene body regions from a transcript database.", "topics": [ "getRegionsFromTxDb" ] }, { "page": "getTx2Gene", "title": "Generate a transcript-to-gene mapping from a GRangesList", "topics": [ "getTx2Gene" ] }, { "page": "plotEISA", "title": "Visualize the results from an exon-intron split analysis.", "topics": [ "plotEISA" ] }, { "page": "runEISA", "title": "Run Exon-Intron Split Analysis.", "topics": [ "runEISA" ] } ], "_readme": "https://github.com/bioc/eisaR/raw/HEAD/README.md", "_rundeps": [ "abind", "Biobase", "BiocGenerics", "DelayedArray", "edgeR", "generics", "GenomicRanges", "IRanges", "lattice", "limma", "locfit", "Matrix", "MatrixGenerics", "matrixStats", "S4Arrays", "S4Vectors", "Seqinfo", "SparseArray", "statmod", "SummarizedExperiment", "XVector" ], "_vignettes": [ { "source": "rna-velocity.Rmd", "filename": "rna-velocity.html", "title": "Generating reference files for spliced and unspliced abundance estimation with alignment-free methods", "author": "Charlotte Soneson", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Generate feature ranges", "Extract feature sequences", "Generate an expanded GTF file", "Generate a transcript-to-gene mapping", "Session info" ], "created": "2020-03-12 16:09:42", "modified": "2025-09-12 13:01:08", "commits": 3 }, { "source": "eisaR.Rmd", "filename": "eisaR.html", "title": "Using eisaR for Exon-Intron Split Analysis (EISA)", "author": "Michael Stadler", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation", "Preparing the annotation", "Quantify RNA-seq alignments in exons and introns", "Align reads", "Count alignments in exons and gene bodies", "Load full count tables", "Run EISA conveniently", "Alternative implementations of EISA", "On the estimation of interactions in a split-plot design experiment", "Visualize EISA results", "Run EISA step-by-step", "Normalization", "Identify quantifiable genes", "Calculate $\\Delta I$, $\\Delta E$ and $\\Delta E - \\Delta I$", "Statistical analysis", "Visualize the results", "Session information", "References" ], "created": "2018-11-29 07:29:23", "modified": "2025-09-12 13:01:08", "commits": 20 } ], "_score": 7.348382756417916, "_indexed": true, "_nocasepkg": "eisar", "_universes": [ "bioc", "mbstadler", "fmicompbio" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.25.0", "date": "2026-07-19T05:57:51.000Z", "distro": "resolute", "commit": "939131c9258887133e733741652c681a45e71d1a", "fileid": "https://r2.ropensci.org/c5d6a89eaccc3491bf7f10af58604c4d9f2f4722685dc531cf907291490d66e5", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29675371280" }, { "r": "4.6.1", "os": "linux", "version": "1.25.0", "date": "2026-07-19T05:56:56.000Z", "distro": "resolute", "commit": "939131c9258887133e733741652c681a45e71d1a", "fileid": "https://r2.ropensci.org/f16f0e08f0d73da7777e437cd3a3f5cdc690bc8331729384fdc9f014ea38fd0c", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29675371280" }, { "r": "4.5.3", "os": "mac", "version": "1.25.0", "date": "2026-07-19T05:55:01.000Z", "commit": "939131c9258887133e733741652c681a45e71d1a", "fileid": "https://r2.ropensci.org/ccc8925947ff4f3882568896c73833b644bec4d6c54f030f533308dea5886344", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29675371280" }, { "r": "4.6.1", "os": "mac", "version": "1.25.0", "date": "2026-07-19T05:55:08.000Z", "commit": "939131c9258887133e733741652c681a45e71d1a", "fileid": "https://r2.ropensci.org/5819430f3242d482d0400d82b7cd2d64b2a03be699bdf8d20ca2704ec1947790", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29675371280" }, { "r": "4.6.0", "os": "wasm", "version": "1.25.0", "date": "2026-07-19T05:56:38.000Z", "commit": "939131c9258887133e733741652c681a45e71d1a", "fileid": "https://r2.ropensci.org/f5d473fd34c125f8640a916b738524b50653be091b45eadb3e437559c7782e61", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29675371280" }, { "r": "4.7.0", "os": "win", "version": "1.25.0", "date": "2026-07-19T05:55:34.000Z", "commit": "939131c9258887133e733741652c681a45e71d1a", "fileid": "https://r2.ropensci.org/4d60a6ec76505d52829e54162b224109e2d2e9c9d25e720140c252b066d5b16a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29675371280" }, { "r": "4.5.3", "os": "win", "version": "1.25.0", "date": "2026-07-19T05:55:36.000Z", "commit": "939131c9258887133e733741652c681a45e71d1a", "fileid": "https://r2.ropensci.org/03f788679a5a82740791e77c7b90b488602b4f1b99fe7710e9cf1976e7f740cc", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29675371280" }, { "r": "4.6.1", "os": "win", "version": "1.25.0", "date": "2026-07-19T05:55:52.000Z", "commit": "939131c9258887133e733741652c681a45e71d1a", "fileid": "https://r2.ropensci.org/e3f4e154d1562bd531f769216ff14439fc173cd68f23fb89b4af2952b63671ac", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29675371280" } ] }