{ "_id": "6a493df9a19c9318096e78df", "Package": "wiggleplotr", "Title": "Make read coverage plots from BigWig files", "Version": "1.37.0", "Authors@R": "person(\"Kaur\", \"Alasoo\", \nemail = \"kaur.alasoo@gmail.com\",\nrole = c(\"aut\", \"cre\"))", "Description": "Tools to visualise read coverage from sequencing\nexperiments together with genomic annotations (genes,\ntranscripts, peaks). Introns of long transcripts can be\nrescaled to a fixed length for better visualisation of exonic\nread coverage.", "License": "Apache License 2.0", "LazyData": "true", "RoxygenNote": "7.2.0", "Encoding": "UTF-8", "VignetteBuilder": "knitr", "biocViews": "ImmunoOncology, Coverage, RNASeq, ChIPSeq, Sequencing,\nVisualization, GeneExpression, Transcription,\nAlternativeSplicing", "Config/pak/sysreqs": "make libbz2-dev liblzma-dev libxml2-dev libssl-dev\nxz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:45:22 UTC", "RemoteUrl": "https://github.com/bioc/wiggleplotr", "RemoteRef": "HEAD", "RemoteSha": "fc07c2398b1dce0c5991f324567b1569ce25bc29", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-04 02:28:14 UTC", "User": "root" }, "Author": "Kaur Alasoo [aut, cre]", "Maintainer": "Kaur Alasoo ", "_user": "bioc", "_type": "src", "_file": "wiggleplotr_1.37.0.tar.gz", "_fileid": "https://r2.ropensci.org/6e5dc0cc30e5bfa07af9fe9e0368279a3c0d6613fbe9d8652544c59a19135561", "_filesize": 917082, "_sha256": "6e5dc0cc30e5bfa07af9fe9e0368279a3c0d6613fbe9d8652544c59a19135561", "_expires": "2026-10-12T17:08:07.000Z", "_created": "2026-07-04T02:28:14.000Z", "_published": "2026-07-04T17:08:09.802Z", "_bioccheck": { "error": 0, "warning": 1, "note": 13 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28692025439", "_status": "success", "_upstream": "https://github.com/bioc/wiggleplotr", "_commit": { "id": "fc07c2398b1dce0c5991f324567b1569ce25bc29", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380322 }, "_maintainer": { "name": "Kaur Alasoo", "email": "kaur.alasoo@gmail.com", "login": "kauralasoo", "twitter": "@kauralasoo", "description": "", "uuid": 508224 }, "_distro": "resolute", "_jobs": [ { "job": 85150843875, "time": 261, "config": "bioc-checks", "r": "4.6.1", "check": "WARNING", "artifact": "8077498097" }, { "job": 85150843835, "time": 351, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "8077507227" }, { "job": 85150843822, "time": 361, "config": "linux-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "8077508234" }, { "job": 85150843904, "time": 178, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "8077488905" }, { "job": 85150843742, "time": 203, "config": "macos-release-arm64", "r": "4.6.1", "check": "WARNING", "artifact": "8077491533" }, { "job": 85150843804, "time": 339, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8077470393" }, { "job": 85150843864, "time": 216, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8077493127" }, { "job": 85150843850, "time": 207, "config": "windows-devel", "r": "4.7.0", "check": "ERROR", "artifact": "8077492138" }, { "job": 85150843897, "time": 208, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "8077492134" }, { "job": 85150843971, "time": 187, "config": "windows-release", "r": "4.6.1", "check": "WARNING", "artifact": "8077489936" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.6", "role": "Depends" }, { "package": "dplyr", "role": "Imports" }, { "package": "ggplot2", "version": ">= 2.2.0", "role": "Imports" }, { "package": "GenomicRanges", "role": "Imports" }, { "package": "rtracklayer", "role": "Imports" }, { "package": "cowplot", "role": "Imports" }, { "package": "assertthat", "role": "Imports" }, { "package": "purrr", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "GenomeInfoDb", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "biomaRt", "role": "Suggests" }, { "package": "GenomicFeatures", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "ensembldb", "role": "Suggests" }, { "package": "EnsDb.Hsapiens.v86", "role": "Suggests" }, { "package": "org.Hs.eg.db", "role": "Suggests" }, { "package": "TxDb.Hsapiens.UCSC.hg38.knownGene", "role": "Suggests" }, { "package": "AnnotationDbi", "role": "Suggests" }, { "package": "AnnotationFilter", "role": "Suggests" }, { "package": "arrow", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 3, "_updates": [ { "week": "2025-41", "n": 3 }, { "week": "2025-42", "n": 1 }, { "week": "2026-12", "n": 2 }, { "week": "2026-13", "n": 1 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.37.0", "bioc": "3.24" }, { "branch": "release", "version": "1.36.0", "bioc": "3.23" } ], "_topics": [ "immunooncology", "coverage", "rnaseq", "chipseq", "sequencing", "visualization", "geneexpression", "transcription", "alternativesplicing" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 445, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_mentions": 4, "_searchresults": 34, "_rbuild": "4.6.1", "_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/wiggleplotr.html", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "extractCoverageData", "getGenotypePalette", "makeManhattanPlot", "plotCoverage", "plotCoverageData", "plotCoverageFromEnsembldb", "plotCoverageFromUCSC", "plotTranscripts", "plotTranscriptsFromEnsembldb", "plotTranscriptsFromUCSC" ], "_datasets": [ { "name": "ncoa7_cdss", "title": "Coding sequences from 9 protein coding transcripts of NCOA7", "object": "ncoa7_cdss", "class": [ "CompressedGRangesList" ], "fields": [], "table": false, "tojson": false }, { "name": "ncoa7_exons", "title": "Exons from 9 protein coding transcripts of NCOA7", "object": "ncoa7_exons", "class": [ "CompressedGRangesList" ], "fields": [], "table": false, "tojson": false }, { "name": "ncoa7_metadata", "title": "Gene metadata for NCOA7", "object": "ncoa7_metadata", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "transcript_id", "gene_id", "gene_name", "strand" ], "rows": 9, "table": true, "tojson": true } ], "_help": [ { "page": "extractCoverageData", "title": "Extract read coverage data from the bigWig files", "topics": [ "extractCoverageData" ] }, { "page": "getGenotypePalette", "title": "Returns a three-colour palette suitable for visualising read coverage stratified by genotype", "topics": [ "getGenotypePalette" ] }, { "page": "makeManhattanPlot", "title": "Make a Manahattan plot of p-values", "topics": [ "makeManhattanPlot" ] }, { "page": "ncoa7_cdss", "title": "Coding sequences from 9 protein coding transcripts of NCOA7", "topics": [ "ncoa7_cdss" ] }, { "page": "ncoa7_exons", "title": "Exons from 9 protein coding transcripts of NCOA7", "topics": [ "ncoa7_exons" ] }, { "page": "ncoa7_metadata", "title": "Gene metadata for NCOA7", "topics": [ "ncoa7_metadata" ] }, { "page": "pasteFactors", "title": "Paste two factors together and preserved their joint order.", "topics": [ "pasteFactors" ] }, { "page": "plotCoverage", "title": "Plot read coverage across a genomic region", "topics": [ "plotCoverage" ] }, { "page": "plotCoverageData", "title": "Plot read coverage across a genomic region", "topics": [ "plotCoverageData" ] }, { "page": "plotCoverageFromEnsembldb", "title": "Plot read coverage directly from ensembldb object.", "topics": [ "plotCoverageFromEnsembldb" ] }, { "page": "plotCoverageFromUCSC", "title": "Plot read coverage directly from UCSC OrgDb and TxDb objects.", "topics": [ "plotCoverageFromUCSC" ] }, { "page": "plotTranscripts", "title": "Quickly plot transcript structure without read coverage tracks", "topics": [ "plotTranscripts" ] }, { "page": "plotTranscriptsFromEnsembldb", "title": "Plot transcripts directly from ensembldb object.", "topics": [ "plotTranscriptsFromEnsembldb" ] }, { "page": "plotTranscriptsFromUCSC", "title": "Plot transcripts directly from UCSC OrgDb and TxDb objects.", "topics": [ "plotTranscriptsFromUCSC" ] }, { "page": "wiggleplotr", "title": "wiggleplotr", "topics": [ "wiggleplotr" ] } ], "_readme": "https://github.com/bioc/wiggleplotr/raw/HEAD/README.md", "_rundeps": [ "abind", "askpass", "assertthat", "BH", "Biobase", "BiocBaseUtils", "BiocGenerics", "BiocIO", "BiocParallel", "Biostrings", "bitops", "cigarillo", "cli", "codetools", "cowplot", "cpp11", "crayon", "curl", "DelayedArray", "dplyr", "farver", "formatR", "futile.logger", "futile.options", "generics", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "ggplot2", "glue", "gtable", "httr", "IRanges", "isoband", "jsonlite", "labeling", "lambda.r", "lattice", "lifecycle", "magrittr", "Matrix", "MatrixGenerics", "matrixStats", "mime", "openssl", "pillar", "pkgconfig", "purrr", "R6", "RColorBrewer", "RCurl", "restfulr", "Rhtslib", "rjson", "rlang", "Rsamtools", "rtracklayer", "S4Arrays", "S4Vectors", "S7", "scales", "Seqinfo", "snow", "SparseArray", "SummarizedExperiment", "sys", "tibble", "tidyselect", "UCSC.utils", "utf8", "vctrs", "viridisLite", "withr", "XML", "XVector", "yaml" ], "_vignettes": [ { "source": "wiggleplotr.Rmd", "filename": "wiggleplotr.html", "title": "Introduction to wiggleplotr", "author": "Kaur Alasoo", "engine": "knitr::rmarkdown", "headings": [ "Extract read coverage from parquet files instead of bigWig files", "Overlaying multiple conditions", "Plotting other types of data", "Extract transcript annotations automatically from Ensembl and UCSC annotations objects" ], "created": "2017-01-07 18:42:45", "modified": "2026-03-18 19:02:54", "commits": 20 } ], "_score": 6.48572142648158, "_indexed": true, "_nocasepkg": "wiggleplotr", "_universes": [ "bioc", "kauralasoo" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.37.0", "date": "2026-07-04T02:33:38.000Z", "distro": "resolute", "commit": "fc07c2398b1dce0c5991f324567b1569ce25bc29", "fileid": "https://r2.ropensci.org/7843404e96f75f0fbe5b104f8ac848d2742e31d1c45d9ad29c85055e8010a30c", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28692025439" }, { "r": "4.6.1", "os": "linux", "version": "1.37.0", "date": "2026-07-04T02:33:34.000Z", "distro": "resolute", "commit": "fc07c2398b1dce0c5991f324567b1569ce25bc29", "fileid": "https://r2.ropensci.org/8de2b8dc5322b9277ee6a3f183734c385ed931c5982b3f03e2c0bfd25c72524f", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28692025439" }, { "r": "4.5.3", "os": "mac", "version": "1.37.0", "date": "2026-07-04T02:30:31.000Z", "commit": "fc07c2398b1dce0c5991f324567b1569ce25bc29", "fileid": "https://r2.ropensci.org/cad181e81d2113b4f01b8751d3d1c1caf4b5ce7f529036e26103ea6b5107536c", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28692025439" }, { "r": "4.6.1", "os": "mac", "version": "1.37.0", "date": "2026-07-04T02:31:02.000Z", "commit": "fc07c2398b1dce0c5991f324567b1569ce25bc29", "fileid": "https://r2.ropensci.org/2aa2e4419c2c4ba46f49d68e114d9caeb84366b1b53443924b2e90e12abdaf78", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28692025439" }, { "r": "4.6.0", "os": "wasm", "version": "1.37.0", "date": "2026-07-04T02:32:05.000Z", "commit": "fc07c2398b1dce0c5991f324567b1569ce25bc29", "fileid": "https://r2.ropensci.org/e25d8bcf33762a292f15d966b7f2edd4024bb5b2253888c371e2e6c64f0c403b", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28692025439" }, { "r": "4.7.0", "os": "win", "version": "1.37.0", "date": "2026-07-04T02:30:52.000Z", "commit": "fc07c2398b1dce0c5991f324567b1569ce25bc29", "fileid": "https://r2.ropensci.org/8ebcd9fc081cd5398c54174fff7f4e6c1f6902ef833281f278d2becb665b9ac1", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28692025439" }, { "r": "4.5.3", "os": "win", "version": "1.37.0", "date": "2026-07-04T02:30:56.000Z", "commit": "fc07c2398b1dce0c5991f324567b1569ce25bc29", "fileid": "https://r2.ropensci.org/f1f5ad1ec96a1448c4c08a16f4769bdcc3eee677fcf68fd57f0a534679760c96", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28692025439" }, { "r": "4.6.1", "os": "win", "version": "1.37.0", "date": "2026-07-04T02:30:39.000Z", "commit": "fc07c2398b1dce0c5991f324567b1569ce25bc29", "fileid": "https://r2.ropensci.org/7bf8d11c659d59eb73de325780947b38b2e81d026ba2e5c2b6beae74e5ce50de", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28692025439" } ] }