{ "_id": "6a1ad2d81d7bb097a09e3205", "Package": "factR", "Title": "Functional Annotation of Custom Transcriptomes", "Version": "1.15.0", "Authors@R": "person(\"Fursham\", \"Hamid\", \nemail = \"fursham.h@gmail.com\",\nrole = c(\"aut\", \"cre\"))", "Description": "factR contain tools to process and interact with\ncustom-assembled transcriptomes (GTF). At its core, factR\nconstructs CDS information on custom transcripts and\nsubsequently predicts its functional output. In addition, factR\nhas tools capable of plotting transcripts, correcting\nchromosome and gene information and shortlisting new\ntranscripts.", "biocViews": "AlternativeSplicing, FunctionalPrediction, GenePrediction", "License": "file LICENSE", "Encoding": "UTF-8", "ByteCompile": "true", "RoxygenNote": "7.2.1", "VignetteBuilder": "knitr", "LazyData": "FALSE", "BiocType": "Software", "URL": "https://fursham-h.github.io/factR/", "Config/pak/sysreqs": "make libbz2-dev libicu-dev liblzma-dev libpng-dev\nlibxml2-dev libssl-dev libx11-dev xz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:58:36 UTC", "RemoteUrl": "https://github.com/bioc/factR", "RemoteRef": "HEAD", "RemoteSha": "4d6b2caa91e8dc47ddc91a12aefd951162e5d189", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 08:35:00 UTC", "User": "root" }, "Author": "Fursham Hamid [aut, cre]", "Maintainer": "Fursham Hamid ", "MD5sum": "55b38c0116824826a35fc20fae5a2300", "_user": "bioc", "_type": "src", "_file": "factR_1.15.0.tar.gz", "_fileid": "e62c048c7df07eca54f278e90d9da6c7acad0ef956bf27d817f583e4fd7dafa5", "_filesize": 1239733, "_sha256": "e62c048c7df07eca54f278e90d9da6c7acad0ef956bf27d817f583e4fd7dafa5", "_created": "2026-05-30T08:35:00.000Z", "_published": "2026-05-30T12:06:48.709Z", "_jobs": [ { "job": 78636932846, "time": 241, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7306890031" }, { "job": 78636932858, "time": 375, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "7306903379" }, { "job": 78636932861, "time": 455, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7306911416" }, { "job": 78636932845, "time": 195, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7308048105" }, { "job": 78636932836, "time": 190, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7308047883" }, { "job": 78636643195, "time": 340, "config": "source", "r": "4.6.0", "check": "ERROR", "artifact": "7306867128" }, { "job": 78636932831, "time": 226, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7306888730" }, { "job": 78636932847, "time": 282, "config": "windows-devel", "r": "4.7.0", "check": "ERROR", "artifact": "7306894124" }, { "job": 78636932859, "time": 304, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7306896330" }, { "job": 78636932865, "time": 283, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7306894106" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 12 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26679260642", "_status": "failure", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/factR", "_commit": { "id": "4d6b2caa91e8dc47ddc91a12aefd951162e5d189", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777381116 }, "_maintainer": { "name": "Fursham Hamid", "email": "fursham.h@gmail.com", "login": "fursham-h", "twitter": "@FurshamH", "description": "Lecturer in Bioinformatics at the Centre for Developmental Neurobiology", "uuid": 37694204 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.2", "role": "Depends" }, { "package": "BiocGenerics", "version": ">= 0.46", "role": "Imports" }, { "package": "Biostrings", "version": ">= 2.68", "role": "Imports" }, { "package": "GenomeInfoDb", "version": ">= 1.36", "role": "Imports" }, { "package": "dplyr", "version": ">= 1.1", "role": "Imports" }, { "package": "GenomicFeatures", "version": ">= 1.52", "role": "Imports" }, { "package": "GenomicRanges", "version": ">= 1.52", "role": "Imports" }, { "package": "IRanges", "version": ">= 2.34", "role": "Imports" }, { "package": "purrr", "version": ">= 1.0", "role": "Imports" }, { "package": "rtracklayer", "version": ">= 1.60", "role": "Imports" }, { "package": "tidyr", "version": ">= 1.3", "role": "Imports" }, { "package": "methods", "version": ">= 4.3", "role": "Imports" }, { "package": "BiocParallel", "version": ">= 1.34", "role": "Imports" }, { "package": "S4Vectors", "version": ">= 0.38", "role": "Imports" }, { "package": "data.table", "version": ">= 1.14", "role": "Imports" }, { "package": "rlang", "version": ">= 1.1", "role": "Imports" }, { "package": "tibble", "version": ">= 3.2", "role": "Imports" }, { "package": "wiggleplotr", "version": ">= 1.24", "role": "Imports" }, { "package": "RCurl", "version": ">= 1.98", "role": "Imports" }, { "package": "XML", "version": ">= 3.99", "role": "Imports" }, { "package": "drawProteins", "version": ">= 1.20", "role": "Imports" }, { "package": "ggplot2", "version": ">= 3.4", "role": "Imports" }, { "package": "stringr", "version": ">= 1.5", "role": "Imports" }, { "package": "pbapply", "version": ">= 1.7", "role": "Imports" }, { "package": "stats", "version": ">= 4.3", "role": "Imports" }, { "package": "utils", "version": ">= 4.3", "role": "Imports" }, { "package": "graphics", "version": ">= 4.3", "role": "Imports" }, { "package": "crayon", "version": ">= 1.5", "role": "Imports" }, { "package": "AnnotationHub", "version": ">= 2.22", "role": "Suggests" }, { "package": "BSgenome", "version": ">= 1.58", "role": "Suggests" }, { "package": "BSgenome.Mmusculus.UCSC.mm10", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "markdown", "role": "Suggests" }, { "package": "zeallot", "role": "Suggests" }, { "package": "rmdformats", "role": "Suggests" }, { "package": "bio3d", "version": ">= 2.4", "role": "Suggests" }, { "package": "signalHsmm", "version": ">= 1.5", "role": "Suggests" }, { "package": "tidyverse", "version": ">= 1.3", "role": "Suggests" }, { "package": "covr", "role": "Suggests" }, { "package": "patchwork", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.15.0", "bioc": "3.24" }, { "branch": "release", "version": "1.14.0", "bioc": "3.23" } ], "_topics": [ "alternativesplicing", "functionalprediction", "geneprediction", "custom-transcriptomes", "functional-annotation", "gtf", "rna-seq-analysis" ], "_stars": 2, "_contributors": [ { "user": "fursham-h", "count": 377, "uuid": 37694204 }, { "user": "jwokaty", "count": 4, "uuid": 1744257 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 293, "source": "https://www.bioconductor.org/packages/stats/bioc/factR" }, "_devurl": "https://github.com/fursham-h/factr", "_pkgdown": "https://fursham-h.github.io/factR/", "_searchresults": 10, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/factR.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/fursham-h/factr", "_realowner": "bioc", "_cranurl": false, "_exports": [ "buildCDS", "filtereach", "has_consistentSeqlevels", "importFASTA", "importGTF", "matchChromosomes", "matchGeneInfo", "mutateeach", "predictDomains", "predictNMD", "sorteach", "subsetNewTranscripts", "trimTranscripts", "viewTranscripts" ], "_datasets": [ { "name": "chrom_matched_query_gtf", "title": "Chromosome matched version of \"query_gtf\"", "object": "chrom_matched_query_gtf", "file": "chrom_matched_query_gtf.rda", "class": [ "GRanges" ], "fields": [], "table": false, "tojson": false }, { "name": "domains.known", "title": "Example output of predictDomains()", "object": "domains.known", "file": "domains.known.rda", "class": [ "data.frame" ], "fields": [ "transcript", "description", "eval", "begin", "end" ], "rows": 85780, "table": true, "tojson": true }, { "name": "domains.out", "title": "Example output of predictDomains()", "object": "domains.out", "file": "domains.out.rda", "class": [ "data.frame" ], "fields": [ "transcript", "description", "eval", "begin", "end" ], "rows": 14880, "table": true, "tojson": true }, { "name": "matched_query_gtf", "title": "Seqlevels and gene_id matched query data", "object": "matched_query_gtf", "file": "matched_query_gtf.rda", "class": [ "GRanges" ], "fields": [], "table": false, "tojson": false }, { "name": "new_query_gtf", "title": "Query data containing CDS information", "object": "new_query_gtf", "file": "new_query_gtf.rda", "class": [ "GRanges" ], "fields": [], "table": false, "tojson": false }, { "name": "query_cds", "title": "CDS from 4 transcripts entries of the same gene", "object": "query_cds", "file": "query_cds.rda", "class": [ "CompressedGRangesList" ], "fields": [], "table": false, "tojson": false }, { "name": "query_exons", "title": "GRangeList of exons from 4 transcripts entries from query_gtf", "object": "query_exons", "file": "query_exons.rda", "class": [ "CompressedGRangesList" ], "fields": [], "table": false, "tojson": false }, { "name": "query_gtf", "title": "Imported GTF file containing 4 transcript entries of the same gene", "object": "query_gtf", "file": "query_gtf.rda", "class": [ "GRanges" ], "fields": [], "table": false, "tojson": false }, { "name": "ref_cds", "title": "CDS from 2 reference transcripts entries of the same gene", "object": "ref_cds", "file": "ref_cds.rda", "class": [ "CompressedGRangesList" ], "fields": [], "table": false, "tojson": false }, { "name": "ref_exons", "title": "Exons from 2 reference transcripts entries of the same gene", "object": "ref_exons", "file": "ref_exons.rda", "class": [ "CompressedGRangesList" ], "fields": [], "table": false, "tojson": false }, { "name": "ref_gtf", "title": "Imported GTF file containing 2 reference transcript entries of the same gene", "object": "ref_gtf", "file": "ref_gtf.rda", "class": [ "GRanges" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "buildCDS", "title": "Reference-guided construction of CDS on GTF object", "topics": [ "buildCDS" ] }, { "page": "chrom_matched_query_gtf", "title": "Chromosome matched version of \"query_gtf\"", "topics": [ "chrom_matched_query_gtf" ] }, { "page": "domains.known", "title": "Example output of predictDomains()", "topics": [ "domains.known" ] }, { "page": "domains.out", "title": "Example output of predictDomains()", "topics": [ "domains.out" ] }, { "page": "filtereach", "title": "Internally filter each element of a GenomicRangesList", "topics": [ "filtereach" ] }, { "page": "has_consistentSeqlevels", "title": "Test consistency of chromosome naming styles (aka seqlevels; e.g. \"chr1\" vs \"1\") across multiple objects", "topics": [ "has_consistentSeqlevels" ] }, { "page": "importFASTA", "title": "Import FASTA file into R", "topics": [ "importFASTA" ] }, { "page": "importGTF", "title": "Import GTF file into R", "topics": [ "importGTF" ] }, { "page": "matchChromosomes", "title": "Match seqlevels of input GRanges to reference GRanges or BioString objects", "topics": [ "matchChromosomes" ] }, { "page": "matched_query_gtf", "title": "Seqlevels and gene_id matched query data", "topics": [ "matched_query_gtf" ] }, { "page": "matchGeneInfo", "title": "Match gene metadata from query GTF to a reference GTF", "topics": [ "matchGeneInfo" ] }, { "page": "mutateeach", "title": "Internally create or transform metadata of a GenomicRangesList", "topics": [ "mutateeach" ] }, { "page": "new_query_gtf", "title": "Query data containing CDS information", "topics": [ "new_query_gtf" ] }, { "page": "predictDomains", "title": "Predict protein domain families from coding transcripts", "topics": [ "predictDomains" ] }, { "page": "predictNMD", "title": "Predict NMD sensitivity on mRNA transcripts", "topics": [ "predictNMD" ] }, { "page": "query_cds", "title": "CDS from 4 transcripts entries of the same gene", "topics": [ "query_cds" ] }, { "page": "query_exons", "title": "GRangeList of exons from 4 transcripts entries from query_gtf", "topics": [ "query_exons" ] }, { "page": "query_gtf", "title": "Imported GTF file containing 4 transcript entries of the same gene", "topics": [ "query_gtf" ] }, { "page": "ref_cds", "title": "CDS from 2 reference transcripts entries of the same gene", "topics": [ "ref_cds" ] }, { "page": "ref_exons", "title": "Exons from 2 reference transcripts entries of the same gene", "topics": [ "ref_exons" ] }, { "page": "ref_gtf", "title": "Imported GTF file containing 2 reference transcript entries of the same gene", "topics": [ "ref_gtf" ] }, { "page": "sorteach", "title": "Internally sort each element of a GenomicRangesList", "topics": [ "sorteach" ] }, { "page": "subsetNewTranscripts", "title": "Shortlist GTF GRanges object for new transcripts", "topics": [ "subsetNewTranscripts" ] }, { "page": "trimTranscripts", "title": "Resize 5' and 3' ends of a transcript GenomicRanges", "topics": [ "trimTranscripts" ] }, { "page": "viewTranscripts", "title": "Plot transcripts directly from GTF.", "topics": [ "viewTranscripts" ] } ], "_readme": "https://github.com/bioc/factR/raw/HEAD/README.md", "_rundeps": [ "abind", "AnnotationDbi", "askpass", "assertthat", "BH", "Biobase", "BiocBaseUtils", "BiocGenerics", "BiocIO", "BiocParallel", "Biostrings", "bit", "bit64", "bitops", "blob", "cachem", "cigarillo", "cli", "clipr", "codetools", "cowplot", "cpp11", "crayon", "curl", "data.table", "DBI", "DelayedArray", "dplyr", "drawProteins", "farver", "fastmap", "formatR", "futile.logger", "futile.options", "generics", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "ggplot2", "glue", "gtable", "hms", "httr", "IRanges", "isoband", "jsonlite", "KEGGREST", "labeling", "lambda.r", "lattice", "lifecycle", "magrittr", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mime", "openssl", "pbapply", "pillar", "pkgconfig", "png", "prettyunits", "progress", "purrr", "R6", "RColorBrewer", "RCurl", "readr", "restfulr", "Rhtslib", "rjson", "rlang", "Rsamtools", "RSQLite", "rtracklayer", "S4Arrays", "S4Vectors", "S7", "scales", "Seqinfo", "snow", "SparseArray", "stringi", "stringr", "SummarizedExperiment", "sys", "tibble", "tidyr", "tidyselect", "tzdb", "UCSC.utils", "utf8", "vctrs", "viridisLite", "vroom", "wiggleplotr", "withr", "XML", "XVector", "yaml" ], "_score": 3.3010299956639813, "_indexed": true, "_nocasepkg": "factr", "_universes": [ "bioc", "fursham-h" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.15.0", "date": "2026-05-30T08:40:09.000Z", "distro": "noble", "commit": "4d6b2caa91e8dc47ddc91a12aefd951162e5d189", "fileid": "e82e5fe22984a51be7630ab79be2ad462a5eb57bb5ed4d67c91a8a5014a6da15", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679260642" }, { "r": "4.6.0", "os": "linux", "version": "1.15.0", "date": "2026-05-30T08:41:24.000Z", "distro": "noble", "commit": "4d6b2caa91e8dc47ddc91a12aefd951162e5d189", "fileid": "25b0dc79b3120161d1482aedd45439f468a90046c8e2f9b1b8828fb8f872afec", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679260642" }, { "r": "4.5.3", "os": "mac", "version": "1.15.0", "date": "2026-05-30T12:05:25.000Z", "commit": "4d6b2caa91e8dc47ddc91a12aefd951162e5d189", "fileid": "9f22d080b6fa328b68f373eb19ffa4ebc21e0d391c635bf81ca84b970b14c5e2", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679260642" }, { "r": "4.6.0", "os": "mac", "version": "1.15.0", "date": "2026-05-30T12:05:22.000Z", "commit": "4d6b2caa91e8dc47ddc91a12aefd951162e5d189", "fileid": "09eaf57612d0662f37da078ff7b3895274eb473664a83b64bd0e4c46b534f501", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679260642" }, { "r": "4.6.0", "os": "wasm", "version": "1.15.0", "date": "2026-05-30T08:39:08.000Z", "commit": "4d6b2caa91e8dc47ddc91a12aefd951162e5d189", "fileid": "c97d68978434c8abe69e1acffbe83c391149218d458ed5f0dd0fb96e97e68bfe", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679260642" }, { "r": "4.7.0", "os": "win", "version": "1.15.0", "date": "2026-05-30T08:38:23.000Z", "commit": "4d6b2caa91e8dc47ddc91a12aefd951162e5d189", "fileid": "13b16ef3af943cb0d9a7971f69123543bda333037dfd01bd3c1ba40fadad25a5", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679260642" }, { "r": "4.5.3", "os": "win", "version": "1.15.0", "date": "2026-05-30T08:39:05.000Z", "commit": "4d6b2caa91e8dc47ddc91a12aefd951162e5d189", "fileid": "053929eba053c6379603c4706d5af9d031ec1c5957ed4532a470a2bfaca124f2", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679260642" }, { "r": "4.6.0", "os": "win", "version": "1.15.0", "date": "2026-05-30T08:38:57.000Z", "commit": "4d6b2caa91e8dc47ddc91a12aefd951162e5d189", "fileid": "d6b6b70ac75c6220bb9e4b64640cb7cf2f5fcd1481459afcdafe571f2ccd6e16", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679260642" } ] }