{ "_id": "6ae9df561e2c7b3a4f5338b6", "Package": "splicelogic", "Title": "splicelogic: differential transcripts to splice events", "Version": "1.1.5", "Authors@R": "c(\nperson(\"Beatriz\", \"Campillo\", email = \"beatrizcampillo29@gmail.com\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-7323-9125\")),\nperson(\"Michael\", \"Love\", email = \"michaelisaiahlove@gmail.com\", role = \"aut\",\ncomment = c(ORCID = \"0000-0001-8401-0545\")),\nperson(\"NIH NHGRI\", role=\"fnd\"),\nperson(\"Wellcome Trust\", role=\"fnd\")\n)", "Description": "Translate differential transcript usage results into\ndiscrete splice events.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "URL": "https://github.com/thelovelab/splicelogic,\nhttps://thelovelab.github.io/splicelogic", "biocViews": "AlternativeSplicing, DifferentialSplicing, Transcriptomics,\nRNASeq, LongRead, Annotation, FunctionalGenomics", "BugReports": "https://github.com/thelovelab/splicelogic/issues", "Config/testthat/edition": "3", "VignetteBuilder": "knitr", "Config/roxygen2/version": "8.1.1", "Config/pak/sysreqs": "make libbz2-dev liblzma-dev libxml2-dev libssl-dev\nxz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-11-02 22:47:09 UTC", "RemoteUrl": "https://github.com/bioc/splicelogic", "RemoteRef": "HEAD", "RemoteSha": "c25b4e6c28280c939a9f7d0295971ef4298ae1a4", "NeedsCompilation": "no", "Packaged": { "Date": "2026-11-03 13:08:46 UTC", "User": "root" }, "Author": "Beatriz Campillo [aut, cre] (ORCID:\n),\nMichael Love [aut] (ORCID: ),\nNIH NHGRI [fnd],\nWellcome Trust [fnd]", "Maintainer": "Beatriz Campillo ", "_user": "bioc", "_type": "src", "_file": "splicelogic_1.1.5.tar.gz", "_fileid": "https://r2.ropensci.org/f38dc714ebb64a1089f9eed343259434c553d76a287607c9b60849c6218e34d3", "_filesize": 222541, "_sha256": "f38dc714ebb64a1089f9eed343259434c553d76a287607c9b60849c6218e34d3", "_expires": "2027-02-11T13:19:16.000Z", "_created": "2026-11-03T13:08:46.000Z", "_published": "2026-11-03T13:19:18.198Z", "_upstream": "https://github.com/bioc/splicelogic", "_status": "failure", "_maintainer": { "name": "Beatriz Campillo", "email": "beatrizcampillo29@gmail.com", "login": "beamimc", "bluesky": "@beamimc.bsky.social", "orcid": "0000-0001-7323-9125", "description": "", "uuid": 59894638 }, "_jobs": [ { "job": 125936951106, "time": 229, "config": "bioc-checks", "r": "4.6.2", "check": "WARNING", "artifact": "13233193525" }, { "job": 125936951070, "time": 529, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "13232979958" }, { "job": 125936951017, "time": 554, "config": "linux-release-x86_64", "r": "4.6.2", "check": "ERROR", "artifact": "13233044975" }, { "job": 125936951122, "time": 336, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "ERROR", "artifact": "13233377170" }, { "job": 125936951015, "time": 380, "config": "macos-release-arm64", "r": "4.6.2", "check": "ERROR", "artifact": "13234080060" }, { "job": 125934121488, "time": 334, "config": "source", "r": "4.6.2", "check": "ERROR", "artifact": "13232832700" }, { "job": 125936951169, "time": 195, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "13232294544" }, { "job": 125936951297, "time": 572, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "13233453797" }, { "job": 125936951076, "time": 380, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "ERROR", "artifact": "13233248965" }, { "job": 125936951128, "time": 417, "config": "windows-release-x86_64", "r": "4.6.2", "check": "ERROR", "artifact": "13232219654" } ], "_bioccheck": { "error": 0, "warning": 1, "note": 5 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/41640932650", "_commit": { "id": "c25b4e6c28280c939a9f7d0295971ef4298ae1a4", "author": "beamimc ", "committer": "beamimc ", "message": "Version Bump to 1.1.5\n", "time": 1793659629 }, "_distro": "resolute", "_host": "GitHub-Actions", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.5.0", "role": "Depends" }, { "package": "plyranges", "role": "Depends" }, { "package": "dplyr", "role": "Imports" }, { "package": "magrittr", "role": "Imports" }, { "package": "GenomicRanges", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "readr", "role": "Suggests" }, { "package": "wiggleplotr", "role": "Suggests" }, { "package": "GenomicFeatures", "role": "Suggests" }, { "package": "AnnotationHub", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "AnnotationDbi", "role": "Suggests" }, { "package": "Seqinfo", "role": "Suggests" }, { "package": "BSgenome", "role": "Suggests" }, { "package": "Biostrings", "role": "Suggests" }, { "package": "BSgenome.Hsapiens.UCSC.hg38", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-46", "n": 10 }, { "week": "2025-47", "n": 3 }, { "week": "2025-50", "n": 1 }, { "week": "2026-05", "n": 1 }, { "week": "2026-06", "n": 14 }, { "week": "2026-07", "n": 13 }, { "week": "2026-08", "n": 15 }, { "week": "2026-09", "n": 15 }, { "week": "2026-10", "n": 10 }, { "week": "2026-11", "n": 14 }, { "week": "2026-12", "n": 40 }, { "week": "2026-13", "n": 1 }, { "week": "2026-16", "n": 12 }, { "week": "2026-18", "n": 2 }, { "week": "2026-19", "n": 10 }, { "week": "2026-20", "n": 8 }, { "week": "2026-21", "n": 10 }, { "week": "2026-31", "n": 7 }, { "week": "2026-32", "n": 1 }, { "week": "2026-33", "n": 3 }, { "week": "2026-34", "n": 9 }, { "week": "2026-35", "n": 8 }, { "week": "2026-36", "n": 18 }, { "week": "2026-39", "n": 3 }, { "week": "2026-42", "n": 5 }, { "week": "2026-44", "n": 4 }, { "week": "2026-45", "n": 6 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.1.4", "bioc": "3.24", "repository": "bioc" }, { "branch": "release", "version": "1.0.1", "bioc": "3.23", "repository": "bioc" } ], "_topics": [ "alternativesplicing", "differentialsplicing", "transcriptomics", "rnaseq", "longread", "annotation", "functionalgenomics", "dtu", "splicing" ], "_stars": 4, "_contributors": [ { "user": "beamimc", "count": 240, "uuid": 59894638 }, { "user": "mikelove", "count": 71, "uuid": 69203 }, { "user": "jtlandis", "count": 3, "uuid": 30324172 }, { "user": "jwokaty", "count": 2, "uuid": 1744257 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 484, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 330, "source": "https://www.bioconductor.org/packages/stats/bioc/splicelogic" }, "_devurl": "https://github.com/thelovelab/splicelogic", "_pkgdown": "https://thelovelab.github.io/splicelogic", "_searchresults": 14, "_rbuild": "4.6.2", "_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/splicelogic.html", "LICENSE" ], "_homeurl": "https://github.com/thelovelab/splicelogic", "_realowner": "bioc", "_cranurl": false, "_exports": [ "create_mock_data", "event_palette", "find_a3ss", "find_a5ss", "find_all_events", "find_alternative_3_prime_splice_sites", "find_alternative_5_prime_splice_sites", "find_alternative_transcription_end_sites", "find_alternative_transcription_start_sites", "find_ates", "find_atss", "find_ie", "find_included_exons", "find_mutually_exclusive_exons", "find_mxe", "find_retained_introns", "find_ri", "find_se", "find_si", "find_skipped_exons", "find_spliced_introns", "generate_a3ss", "generate_a5ss", "generate_ates", "generate_atss", "generate_mxe", "generate_ri", "generate_se", "get_seq", "plot_transcript_lfc", "plot_transcripts", "plot_transcripts_by_gene", "plot_transcripts_by_pair", "prepare_exons", "prepare_exons_by_partition", "preprocess" ], "_help": [ { "page": "splicelogic-package", "title": "splicelogic: differential transcripts to splice events", "topics": [ "splicelogic-package", "splicelogic" ] }, { "page": "create_mock_data", "title": "Create mock GRanges data for splicing event testing", "topics": [ "create_mock_data" ] }, { "page": "event_palette", "title": "Default fill colours for splicelogic event types", "topics": [ "event_palette" ] }, { "page": "find_events", "title": "Find splice events from annotated exons", "topics": [ "find_a3ss", "find_a5ss", "find_all_events", "find_alternative_3_prime_splice_sites", "find_alternative_5_prime_splice_sites", "find_alternative_transcription_end_sites", "find_alternative_transcription_start_sites", "find_ates", "find_atss", "find_events", "find_ie", "find_included_exons", "find_mutually_exclusive_exons", "find_mxe", "find_retained_introns", "find_ri", "find_se", "find_si", "find_skipped_exons", "find_spliced_introns" ] }, { "page": "generate_events", "title": "Generate mock splice events in a GRanges object", "topics": [ "generate_a3ss", "generate_a5ss", "generate_ates", "generate_atss", "generate_events", "generate_mxe", "generate_ri", "generate_se" ] }, { "page": "get_seq", "title": "Extract sequences for GRanges", "topics": [ "get_seq" ] }, { "page": "plot_transcript_lfc", "title": "Plot a per-transcript fold change for the transcripts of splicelogic events", "topics": [ "plot_transcript_lfc" ] }, { "page": "plot_transcripts", "title": "Plot the transcripts involved in splicelogic events", "topics": [ "plot_transcripts" ] }, { "page": "plot_transcripts_by_gene", "title": "Plot the transcripts involved in splicelogic events, one plot per gene", "topics": [ "plot_transcripts_by_gene" ] }, { "page": "plot_transcripts_by_pair", "title": "Plot the transcripts involved in splicelogic events, one plot per pair", "topics": [ "plot_transcripts_by_pair" ] }, { "page": "prepare_exons", "title": "Prepare exon ranges from a TxDb and DTU results table", "topics": [ "prepare_exons" ] }, { "page": "prepare_exons_by_partition", "title": "Prepare exons from two transcript partitions", "topics": [ "prepare_exons_by_partition" ] }, { "page": "preprocess", "title": "Preprocess input GRanges object for splicing event calculation", "topics": [ "preprocess" ] } ], "_readme": "https://github.com/bioc/splicelogic/raw/HEAD/README.md", "_rundeps": [ "askpass", "BH", "BiocBaseUtils", "BiocGenerics", "BiocIO", "BiocParallel", "Biostrings", "bitops", "cigarillo", "cli", "codetools", "cpp11", "crayon", "curl", "dplyr", "formatR", "futile.logger", "futile.options", "generics", "GenomicAlignments", "GenomicRanges", "glue", "httr", "IRanges", "jsonlite", "lambda.r", "lifecycle", "magrittr", "mime", "openssl", "pillar", "pkgconfig", "plyranges", "R6", "RCurl", "restfulr", "Rhtslib", "rjson", "rlang", "Rsamtools", "rtracklayer", "S4Vectors", "Seqinfo", "snow", "sys", "tibble", "tidyselect", "utf8", "vctrs", "withr", "XML", "XVector", "yaml" ], "_score": 5.355643050220869, "_indexed": true, "_nocasepkg": "splicelogic", "_universes": [ "bioc", "beamimc", "thelovelab" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.1.5", "date": "2026-11-03T13:14:57.000Z", "distro": "resolute", "commit": "c25b4e6c28280c939a9f7d0295971ef4298ae1a4", "fileid": "https://r2.ropensci.org/da28ea5e9f63201ac816a7fb1391fb012f0baa90b68cfb4051469213f1426089", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41640932650" }, { "r": "4.6.2", "os": "linux", "version": "1.1.5", "date": "2026-11-03T13:15:51.000Z", "distro": "resolute", "commit": "c25b4e6c28280c939a9f7d0295971ef4298ae1a4", "fileid": "https://r2.ropensci.org/3613198360a11910d9a8303a4c0be002685743d1586ab56ab6717a4d66d748f4", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41640932650" }, { "r": "4.5.3", "os": "mac", "version": "1.1.5", "date": "2026-11-03T13:11:42.000Z", "commit": "c25b4e6c28280c939a9f7d0295971ef4298ae1a4", "fileid": "https://r2.ropensci.org/0819076b5a3a4b461a1f163fceec5586ee7352ad57e3ab6baba90ef55e4ab8ae", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41640932650" }, { "r": "4.6.2", "os": "mac", "version": "1.1.5", "date": "2026-11-03T13:11:59.000Z", "commit": "c25b4e6c28280c939a9f7d0295971ef4298ae1a4", "fileid": "https://r2.ropensci.org/7762378c940af6cbe87e900bf4f77d8f310622c94e0b79c3b59d59b4854ac51d", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41640932650" }, { "r": "4.6.0", "os": "wasm", "version": "1.1.5", "date": "2026-11-03T13:12:29.000Z", "commit": "c25b4e6c28280c939a9f7d0295971ef4298ae1a4", "fileid": "https://r2.ropensci.org/1e1e5349b8c3b64b88e0d4e325f3697e7bb946f6686643a049924fcb44414fee", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41640932650" }, { "r": "4.7.0", "os": "win", "version": "1.1.5", "date": "2026-11-03T13:14:33.000Z", "commit": "c25b4e6c28280c939a9f7d0295971ef4298ae1a4", "fileid": "https://r2.ropensci.org/f8b0f51eb6ce6e3a0bee6363cf59f64168edfc7b6505e1c556db612c2f978ce8", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41640932650" }, { "r": "4.5.3", "os": "win", "version": "1.1.5", "date": "2026-11-03T13:11:32.000Z", "commit": "c25b4e6c28280c939a9f7d0295971ef4298ae1a4", "fileid": "https://r2.ropensci.org/d7c42c0b03f1eaa88581bd5cd49a58ff4d25019bb439644c200d535094956854", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41640932650" }, { "r": "4.6.2", "os": "win", "version": "1.1.5", "date": "2026-11-03T13:12:55.000Z", "commit": "c25b4e6c28280c939a9f7d0295971ef4298ae1a4", "fileid": "https://r2.ropensci.org/f96f6aef4bc4b292412a38912b639fb8b0ac36f8594f14752f4b7b68a7f0ab42", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41640932650" } ] }