{ "_id": "6a1ad04a1d7bb097a09e1553", "Package": "GeneStructureTools", "Type": "Package", "Title": "Tools for spliced gene structure manipulation and analysis", "Version": "1.33.0", "Author": "Beth Signal", "Maintainer": "Beth Signal ", "Description": "GeneStructureTools can be used to create in silico\nalternative splicing events, and analyse potential effects this\nhas on functional gene products.", "License": "BSD_3_clause + file LICENSE", "Encoding": "UTF-8", "VignetteBuilder": "knitr", "RoxygenNote": "6.0.1", "biocViews": "ImmunoOncology, Software, DifferentialSplicing,\nFunctionalPrediction, Transcriptomics, AlternativeSplicing,\nRNASeq", "Config/pak/sysreqs": "cmake make libbz2-dev libicu-dev libjpeg-dev\nliblzma-dev libpng-dev libuv1-dev libxml2-dev libssl-dev\nxz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:47:25 UTC", "RemoteUrl": "https://github.com/bioc/GeneStructureTools", "RemoteRef": "HEAD", "RemoteSha": "bfdeb062cea8860318d577ff10f8099cc46cd706", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 08:18:53 UTC", "User": "root" }, "MD5sum": "33bfd6dfa6ee70cb5a550840905a4d82", "_user": "bioc", "_type": "src", "_file": "GeneStructureTools_1.33.0.tar.gz", "_fileid": "5546917307cdb434f832a9ac7afb82249bc9949315afba876514a45586a9d746", "_filesize": 2957893, "_sha256": "5546917307cdb434f832a9ac7afb82249bc9949315afba876514a45586a9d746", "_created": "2026-05-30T08:18:53.000Z", "_published": "2026-05-30T11:55:54.574Z", "_jobs": [ { "job": 78636152547, "time": 274, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7306805015" }, { "job": 78636152539, "time": 559, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7306832452" }, { "job": 78636152534, "time": 568, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7306833135" }, { "job": 78636152545, "time": 304, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7307990428" }, { "job": 78636152555, "time": 302, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7307991077" }, { "job": 78635801158, "time": 420, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7306777651" }, { "job": 78636152544, "time": 224, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7306800164" }, { "job": 78636152552, "time": 509, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7306827811" }, { "job": 78636152560, "time": 403, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7306817297" }, { "job": 78636152557, "time": 499, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7306826883" } ], "_bioccheck": { "error": 1, "warning": 1, "note": 13 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26678941242", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/GeneStructureTools", "_commit": { "id": "bfdeb062cea8860318d577ff10f8099cc46cd706", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380445 }, "_maintainer": { "name": "Beth Signal", "email": "b.signal@garvan.org.au" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "Biostrings", "role": "Imports" }, { "package": "GenomicRanges", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "plyr", "role": "Imports" }, { "package": "stringdist", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "BSgenome.Mmusculus.UCSC.mm10", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "Gviz", "role": "Imports" }, { "package": "rtracklayer", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.33.0", "bioc": "3.24" }, { "branch": "release", "version": "1.32.0", "bioc": "3.23" } ], "_topics": [ "immunooncology", "software", "differentialsplicing", "functionalprediction", "transcriptomics", "alternativesplicing", "rnaseq" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 444, "source": "https://www.bioconductor.org/packages/stats/bioc/GeneStructureTools" }, "_searchresults": 22, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/GeneStructureTools.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "addBroadTypes", "addIntronInTranscript", "alternativeIntronUsage", "annotateGeneModel", "attrChangeAltSpliced", "coordinates", "DEXSeqIdsToGeneIds", "diffSplicingResults", "exonsToTranscripts", "filterGtfOverlap", "filterWhippetEvents", "findDEXexonType", "findExonContainingTranscripts", "findIntronContainingTranscripts", "findJunctionPairs", "formatWhippetEvents", "getOrfs", "getUOrfs", "junctions", "leafcutterTranscriptChangeSummary", "makeGeneModel", "maxLocation", "orfDiff", "orfSimilarity", "overlapTypes", "readCounts", "readWhippetDataSet", "readWhippetDIFFfiles", "readWhippetJNCfiles", "readWhippetPSIfiles", "removeDuplicateTranscripts", "removeSameExon", "removeVersion", "reorderExonNumbers", "replaceJunction", "skipExonInTranscript", "summariseExonTypes", "transcriptChangeSummary", "UTR2UTR53", "whippetTranscriptChangeSummary" ], "_help": [ { "page": "addBroadTypes", "title": "Change transcript biotypes to a broader set", "topics": [ "addBroadTypes" ] }, { "page": "addIntronInTranscript", "title": "Add a retained intron to the transcripts it is skipped by", "topics": [ "addIntronInTranscript" ] }, { "page": "alternativeIntronUsage", "title": "Create transcripts with alternative intron usage", "topics": [ "alternativeIntronUsage" ] }, { "page": "annotateGeneModel", "title": "Annotate a GRanges gene model with ORF boundries for visualisation with Gviz", "topics": [ "annotateGeneModel" ] }, { "page": "attrChangeAltSpliced", "title": "Evaluate the change in an attribute between a set of 'normal' transcripts and 'alternative' transcripts", "topics": [ "attrChangeAltSpliced" ] }, { "page": "coordinates-methods", "title": "Method coordinates", "topics": [ "coordinates", "coordinates,whippetDataSet-method" ] }, { "page": "DEXSeqIdsToGeneIds", "title": "Convert DEXSeq ids to gene ids", "topics": [ "DEXSeqIdsToGeneIds" ] }, { "page": "diffSplicingResults-methods", "title": "Method diffSplicingResults", "topics": [ "diffSplicingResults", "diffSplicingResults,whippetDataSet-method" ] }, { "page": "exonsToTranscripts", "title": "Convert an exon-level gtf annotation to a transcript-level gtf annotation", "topics": [ "exonsToTranscripts" ] }, { "page": "filterGtfOverlap", "title": "Filter a GTF overlap to remove exons when exon is annotated as a CDS/UTR", "topics": [ "filterGtfOverlap" ] }, { "page": "filterWhippetEvents", "title": "Filter out significant events from a whippet diff comparison", "topics": [ "filterWhippetEvents" ] }, { "page": "findDEXexonType", "title": "Find a DEXSeq exons' biotype", "topics": [ "findDEXexonType" ] }, { "page": "findExonContainingTranscripts", "title": "Given the location of a whole spliced in exon, find transcripts which can splice out this exon", "topics": [ "findExonContainingTranscripts" ] }, { "page": "findIntronContainingTranscripts", "title": "Given the location of a whole retained intron, find transcripts which splice out this intron", "topics": [ "findIntronContainingTranscripts" ] }, { "page": "findJunctionPairs", "title": "Find alternative junctions for Whippet alternative splicing events", "topics": [ "findJunctionPairs" ] }, { "page": "formatWhippetEvents", "title": "Format Whippet co-ordinates as a GRanges object", "topics": [ "formatWhippetEvents" ] }, { "page": "getOrfs", "title": "Get open reading frames for transcripts", "topics": [ "getOrfs" ] }, { "page": "getUOrfs", "title": "Get upstream open reading frames for transcripts with annotated main ORFs", "topics": [ "getUOrfs" ] }, { "page": "junctions-methods", "title": "Method junctions", "topics": [ "junctions", "junctions,whippetDataSet-method" ] }, { "page": "leafcutterTranscriptChangeSummary", "title": "Compare open reading frames for whippet differentially spliced events", "topics": [ "leafcutterTranscriptChangeSummary" ] }, { "page": "makeGeneModel", "title": "Convert GRanges gene model to data.frame for visualisation with Gviz", "topics": [ "makeGeneModel" ] }, { "page": "maxLocation", "title": "Find the largest distance between two vectors of numbers Helper function for get_orfs", "topics": [ "maxLocation" ] }, { "page": "orfDiff", "title": "Evaluate changes to ORFs caused by alternative splicing", "topics": [ "orfDiff" ] }, { "page": "orfSimilarity", "title": "calculate percentage of orfB contained in orfA", "topics": [ "orfSimilarity" ] }, { "page": "overlapTypes", "title": "Annotate introns and exonic parts by overlaping exon biotype", "topics": [ "overlapTypes" ] }, { "page": "readCounts-methods", "title": "Method readCounts", "topics": [ "readCounts", "readCounts,whippetDataSet-method" ] }, { "page": "readWhippetDataSet", "title": "Import whippet results files as a whippetDataSet", "topics": [ "readWhippetDataSet" ] }, { "page": "readWhippetDIFFfiles", "title": "Read in a list of whippet .diff.gz files and format as a data.frame", "topics": [ "readWhippetDIFFfiles" ] }, { "page": "readWhippetJNCfiles", "title": "Read in a list of whippet .jnc.gz files and format as a GRanges object", "topics": [ "readWhippetJNCfiles" ] }, { "page": "readWhippetPSIfiles", "title": "Read in a list of whippet .psi.gz files and format as a data.frame", "topics": [ "readWhippetPSIfiles" ] }, { "page": "removeDuplicateTranscripts", "title": "Remove transcript duplicates", "topics": [ "removeDuplicateTranscripts" ] }, { "page": "removeSameExon", "title": "Remove exon duplicates", "topics": [ "removeSameExon" ] }, { "page": "removeVersion", "title": "Remove version number from ensembl gene/transcript ids", "topics": [ "removeVersion" ] }, { "page": "reorderExonNumbers", "title": "Reorder the exon numbers in a gtf annotation", "topics": [ "reorderExonNumbers" ] }, { "page": "replaceJunction", "title": "Find transcripts containing/overlapping junctions and replace them with alternative junctions", "topics": [ "replaceJunction" ] }, { "page": "skipExonInTranscript", "title": "Remove and include a skipped exon from the transcripts it overlaps", "topics": [ "skipExonInTranscript" ] }, { "page": "summariseExonTypes", "title": "Summarise exon biotypes to broader categories", "topics": [ "summariseExonTypes" ] }, { "page": "transcriptChangeSummary", "title": "Compare open reading frames for two sets of paired transcripts", "topics": [ "transcriptChangeSummary" ] }, { "page": "UTR2UTR53", "title": "Annotate UTRs from Gencode GTF as 5' or 3'", "topics": [ "UTR2UTR53" ] }, { "page": "whippetDataSet-class", "title": "Class whippetDataSet", "topics": [ "whippetDataSet-class" ] }, { "page": "whippetTranscriptChangeSummary", "title": "Compare open reading frames for whippet differentially spliced events", "topics": [ "whippetTranscriptChangeSummary" ] } ], "_readme": "https://github.com/bioc/GeneStructureTools/raw/HEAD/README.md", "_rundeps": [ "abind", "AnnotationDbi", "AnnotationFilter", "askpass", "backports", "base64enc", "BH", "Biobase", "BiocBaseUtils", "BiocFileCache", "BiocGenerics", "BiocIO", "BiocParallel", "biomaRt", "Biostrings", "biovizBase", "bit", "bit64", "bitops", "blob", "BSgenome", "BSgenome.Mmusculus.UCSC.mm10", "bslib", "cachem", "checkmate", "cigarillo", "cli", "cluster", "codetools", "colorspace", "cpp11", "crayon", "curl", "data.table", "DBI", "dbplyr", "DelayedArray", "deldir", "dichromat", "digest", "dplyr", "ensembldb", "evaluate", "farver", "fastmap", "filelock", "fontawesome", "foreign", "formatR", "Formula", "fs", "futile.logger", "futile.options", "generics", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "ggplot2", "glue", "gridExtra", "gtable", "Gviz", "highr", "Hmisc", "hms", "htmlTable", "htmltools", "htmlwidgets", "httr", "httr2", "interp", "IRanges", "isoband", "jpeg", "jquerylib", "jsonlite", "KEGGREST", "knitr", "labeling", "lambda.r", "lattice", "latticeExtra", "lazyeval", "lifecycle", "magrittr", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mime", "nnet", "openssl", "pillar", "pkgconfig", "plyr", "png", "prettyunits", "progress", "ProtGenerics", "purrr", "R6", "rappdirs", "RColorBrewer", "Rcpp", "RcppEigen", "RCurl", "restfulr", "Rhtslib", "rjson", "rlang", "rmarkdown", "rpart", "Rsamtools", "RSQLite", "rstudioapi", "rtracklayer", "S4Arrays", "S4Vectors", "S7", "sass", "scales", "Seqinfo", "snow", "SparseArray", "stringdist", "stringi", "stringr", "SummarizedExperiment", "sys", "tibble", "tidyr", "tidyselect", "tinytex", "UCSC.utils", "utf8", "VariantAnnotation", "vctrs", "viridisLite", "withr", "xfun", "XML", "xml2", "XVector", "yaml" ], "_vignettes": [ { "source": "Vignette.Rmd", "filename": "Vignette.html", "title": "Introduction to GeneStructureTools", "author": "Beth Signal", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Importing Differential Splicing Data", "Whippet", "leafcutter", "Summarise changes in gene structures due to splicing", "Altering Gene and Transcript Structures", "Exon skipping", "Intron Retention", "Alternative acceptor and donor splice sites", "Aternative acceptor", "Aternative donor", "Alternative first/last exons", "Alternative first exons", "Alternative last exons", "Alternative Intron usage (leafcutter)", "Annotate Open Reading Frames", "DEXSeq", "GTF reannotation", "DEXSeq event overlapping", "Session Info" ], "created": "2018-01-10 03:42:13", "modified": "2018-03-12 02:34:30", "commits": 11 } ], "_score": 4.342422680822207, "_indexed": true, "_nocasepkg": "genestructuretools", "_universes": [ "bioc" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.33.0", "date": "2026-05-30T08:23:49.000Z", "distro": "noble", "commit": "bfdeb062cea8860318d577ff10f8099cc46cd706", "fileid": "a931519731c7fab73f0f980b50f7d0092711fc9bebed2402c734f06d7c98c6cf", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678941242" }, { "r": "4.6.0", "os": "linux", "version": "1.33.0", "date": "2026-05-30T08:24:27.000Z", "distro": "noble", "commit": "bfdeb062cea8860318d577ff10f8099cc46cd706", "fileid": "239e7e1bd09cac8955424eb835396877bcde7d529a900aabd17963390a0814e6", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678941242" }, { "r": "4.5.3", "os": "mac", "version": "1.33.0", "date": "2026-05-30T11:52:39.000Z", "commit": "bfdeb062cea8860318d577ff10f8099cc46cd706", "fileid": "b3d28c27ebd5984ce7c5eb6e1f60d37e60c2c51cf75bc3fdafc890091e3d6513", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678941242" }, { "r": "4.6.0", "os": "mac", "version": "1.33.0", "date": "2026-05-30T11:52:26.000Z", "commit": "bfdeb062cea8860318d577ff10f8099cc46cd706", "fileid": "8dfc7a00c449642e422d4d564d6dcaccfec6d543d5e4460974db6c80a8f62ae5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678941242" }, { "r": "4.6.0", "os": "wasm", "version": "1.33.0", "date": "2026-05-30T08:23:32.000Z", "commit": "bfdeb062cea8860318d577ff10f8099cc46cd706", "fileid": "8f3fb5d482975aea8183cbcf726dbcb05bc793cc5c87d6cead273b0e812bc2bf", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678941242" }, { "r": "4.7.0", "os": "win", "version": "1.33.0", "date": "2026-05-30T08:22:18.000Z", "commit": "bfdeb062cea8860318d577ff10f8099cc46cd706", "fileid": "5d95a8b4d4fa8dec8c9774f6771ffb1bfdc927a7a9acd3f5e63b5bf9c66deaa2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678941242" }, { "r": "4.5.3", "os": "win", "version": "1.33.0", "date": "2026-05-30T08:22:14.000Z", "commit": "bfdeb062cea8860318d577ff10f8099cc46cd706", "fileid": "1c6c203b8de5921163115117ade8f7129d414349754d44e057c6e671e7a4e2b6", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678941242" }, { "r": "4.6.0", "os": "win", "version": "1.33.0", "date": "2026-05-30T08:22:23.000Z", "commit": "bfdeb062cea8860318d577ff10f8099cc46cd706", "fileid": "2d28390e58e39ea8488c1df419f5687a337ee009b4a20ffa1416fea9e69fb006", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678941242" } ] }