{ "_id": "6a1be9df1d7bb097a0a1db7b", "Package": "regionReport", "Type": "Package", "Title": "Generate HTML or PDF reports for a set of genomic regions or\nDESeq2/edgeR results", "Version": "1.46.0", "Date": "2025-07-22", "Authors@R": "c(person(\"Leonardo\", \"Collado-Torres\", role = c(\"aut\", \"cre\"), email\n= \"lcolladotor@gmail.com\", comment = c(ORCID = \"0000-0003-2140-308X\")),\nperson(c(\"Andrew\", \"E.\"), \"Jaffe\", role = \"aut\",\nemail = \"andrew.jaffe@libd.org\", comment = c(ORCID = \"0000-0001-6886-1454\")),\nperson(c(\"Jeffrey\", \"T.\"), \"Leek\", role = c(\"aut\", \"ths\"),\nemail = \"jtleek@gmail.com\", comment = c(ORCID = \"0000-0002-2873-2671\")))", "Description": "Generate HTML or PDF reports to explore a set of regions\nsuch as the results from annotation-agnostic expression\nanalysis of RNA-seq data at base-pair resolution performed by\nderfinder. You can also create reports for DESeq2 or edgeR\nresults.", "License": "Artistic-2.0", "URL": "https://github.com/leekgroup/regionReport", "BugReports": "https://support.bioconductor.org/t/regionReport/", "VignetteBuilder": "knitr", "biocViews": "DifferentialExpression, Sequencing, RNASeq, Software,\nVisualization, Transcription, Coverage, ReportWriting,\nDifferentialMethylation, DifferentialPeakCalling,\nImmunoOncology, QualityControl", "RoxygenNote": "7.3.2", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "Config/pak/sysreqs": "cmake make libbz2-dev libicu-dev liblzma-dev\nlibpng-dev libuv1-dev libxml2-dev libssl-dev xz-utils\nzlib1g-dev", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 12:39:52 UTC", "RemoteUrl": "https://github.com/bioc/regionReport", "RemoteRef": "RELEASE_3_23", "RemoteSha": "0b5727526bcfef664522bde1f681ce5ee2add101", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-31 06:43:34 UTC", "User": "root" }, "Author": "Leonardo Collado-Torres [aut, cre] (ORCID:\n),\nAndrew E. Jaffe [aut] (ORCID: ),\nJeffrey T. Leek [aut, ths] (ORCID:\n)", "Maintainer": "Leonardo Collado-Torres ", "MD5sum": "deb9212831997685ca6120992d123b32", "_user": "bioc-release", "_type": "src", "_file": "regionReport_1.46.0.tar.gz", "_fileid": "eebbbbfec8cbfc235a98d2bf7b8b10db7145fc8ab789a5ae9687d930638f1f82", "_filesize": 233153, "_sha256": "eebbbbfec8cbfc235a98d2bf7b8b10db7145fc8ab789a5ae9687d930638f1f82", "_created": "2026-05-31T06:43:34.000Z", "_published": "2026-05-31T07:57:19.759Z", "_jobs": [ { "job": 78706407067, "time": 292, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7314557282" }, { "job": 78706407080, "time": 752, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7314602837" }, { "job": 78706407076, "time": 763, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7314603913" }, { "job": 78706407077, "time": 475, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7314992377" }, { "job": 78706407082, "time": 632, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7315009559" }, { "job": 78706028579, "time": 454, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7314527680" }, { "job": 78706407068, "time": 246, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7314552367" }, { "job": 78706407087, "time": 832, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7314611380" }, { "job": 78706407089, "time": 763, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7314604063" }, { "job": 78706407084, "time": 906, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7314619394" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 8 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26705532136", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/regionReport", "_commit": { "id": "0b5727526bcfef664522bde1f681ce5ee2add101", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n", "time": 1777379992 }, "_maintainer": { "name": "Leonardo Collado-Torres", "email": "lcolladotor@gmail.com", "login": "lcolladotor", "bluesky": "@lcolladotor.bsky.social", "linkedin": "in/lcollado", "twitter": "@lcolladotor", "description": "Find more information about myself at my website where I post my recent publications, talks, blog posts and other updates.", "uuid": 2288213, "orcid": "0000-0003-2140-308X" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.2", "role": "Depends" }, { "package": "BiocStyle", "version": ">= 2.5.19", "role": "Imports" }, { "package": "derfinder", "version": ">= 1.25.3", "role": "Imports" }, { "package": "DEFormats", "role": "Imports" }, { "package": "DESeq2", "role": "Imports" }, { "package": "Seqinfo", "role": "Imports" }, { "package": "GenomeInfoDb", "role": "Imports" }, { "package": "GenomicRanges", "role": "Imports" }, { "package": "knitr", "version": ">= 1.6", "role": "Imports" }, { "package": "knitrBootstrap", "version": ">= 0.9.0", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "RefManageR", "role": "Imports" }, { "package": "rmarkdown", "version": ">= 0.9.5", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "BiocManager", "role": "Suggests" }, { "package": "biovizBase", "role": "Suggests" }, { "package": "bumphunter", "version": ">= 1.7.6", "role": "Suggests" }, { "package": "derfinderPlot", "version": ">= 1.29.1", "role": "Suggests" }, { "package": "sessioninfo", "role": "Suggests" }, { "package": "DT", "role": "Suggests" }, { "package": "edgeR", "role": "Suggests" }, { "package": "ggbio", "version": ">= 1.35.2", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "grid", "role": "Suggests" }, { "package": "gridExtra", "role": "Suggests" }, { "package": "IRanges", "role": "Suggests" }, { "package": "mgcv", "role": "Suggests" }, { "package": "pasilla", "role": "Suggests" }, { "package": "pheatmap", "role": "Suggests" }, { "package": "RColorBrewer", "role": "Suggests" }, { "package": "TxDb.Hsapiens.UCSC.hg19.knownGene", "role": "Suggests" }, { "package": "whisker", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-30", "n": 2 }, { "week": "2025-44", "n": 2 }, { "week": "2026-14", "n": 1 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.47.0", "bioc": "3.24" }, { "branch": "release", "version": "1.46.0", "bioc": "3.23" } ], "_topics": [ "differentialexpression", "sequencing", "rnaseq", "software", "visualization", "transcription", "coverage", "reportwriting", "differentialmethylation", "differentialpeakcalling", "immunooncology", "qualitycontrol", "bioconductor", "derfinder", "deseq2", "edger", "regionreport", "rmarkdown" ], "_stars": 9, "_contributors": [ { "user": "lcolladotor", "count": 492, "uuid": 2288213 }, { "user": "nturaga", "count": 14, "uuid": 2746443 }, { "user": "jwokaty", "count": 14, "uuid": 1744257 }, { "user": "dtenenba", "count": 10, "uuid": 2286826 }, { "user": "hpages", "count": 4, "uuid": 8810451 }, { "user": "vobencha", "count": 2, "uuid": 2466173 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 508, "source": "https://www.bioconductor.org/packages/stats/bioc/regionReport" }, "_mentions": 2, "_devurl": "https://github.com/leekgroup/regionreport", "_searchresults": 52, "_rbuild": "4.6.0", "_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/regionReport.html", "manual.pdf" ], "_homeurl": "https://github.com/leekgroup/regionreport", "_realowner": "bioc", "_cranurl": false, "_exports": [ "derfinderReport", "DESeq2Report", "edgeReport", "renderReport", "templateDensity", "templateHistogram", "templateManhattan", "templatePvalueDensity", "templatePvalueHistogram" ], "_help": [ { "page": "derfinderReport", "title": "Generate a HTML/PDF report exploring the basic results from derfinder", "topics": [ "derfinderReport" ] }, { "page": "DESeq2Report", "title": "Generate a HTML/PDF report exploring DESeq2 results", "topics": [ "DESeq2Report" ] }, { "page": "edgeReport", "title": "Generate a HTML/PDF report exploring edgeR results", "topics": [ "edgeReport" ] }, { "page": "renderReport", "title": "Generate a HTML/PDF report exploring a set of genomic regions", "topics": [ "renderReport", "templateDensity", "templateHistogram", "templateManhattan", "templatePvalueDensity", "templatePvalueHistogram" ] } ], "_readme": "https://github.com/bioc/regionReport/raw/RELEASE_3_23/README.md", "_rundeps": [ "abind", "AnnotationDbi", "askpass", "backports", "base64enc", "BH", "bibtex", "Biobase", "BiocBaseUtils", "BiocGenerics", "BiocIO", "BiocManager", "BiocParallel", "BiocStyle", "Biostrings", "bit", "bit64", "bitops", "blob", "bookdown", "BSgenome", "bslib", "bumphunter", "cachem", "checkmate", "cigarillo", "cli", "cluster", "codetools", "colorspace", "commonmark", "cpp11", "crayon", "curl", "data.table", "DBI", "DEFormats", "DelayedArray", "derfinder", "derfinderHelper", "DESeq2", "digest", "doRNG", "edgeR", "evaluate", "farver", "fastmap", "fontawesome", "foreach", "foreign", "formatR", "Formula", "fs", "futile.logger", "futile.options", "generics", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicFiles", "GenomicRanges", "ggplot2", "glue", "gridExtra", "gtable", "highr", "Hmisc", "htmlTable", "htmltools", "htmlwidgets", "httr", "IRanges", "isoband", "iterators", "jquerylib", "jsonlite", "KEGGREST", "knitr", "knitrBootstrap", "labeling", "lambda.r", "lattice", "lifecycle", "limma", "litedown", "locfit", "lubridate", "magrittr", "markdown", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mime", "nnet", "openssl", "pkgconfig", "plyr", "png", "qvalue", "R6", "rappdirs", "RColorBrewer", "Rcpp", "RcppArmadillo", "RCurl", "RefManageR", "reshape2", "restfulr", "Rhtslib", "rjson", "rlang", "rmarkdown", "rngtools", "rpart", "Rsamtools", "RSQLite", "rstudioapi", "rtracklayer", "S4Arrays", "S4Vectors", "S7", "sass", "scales", "Seqinfo", "snow", "SparseArray", "statmod", "stringi", "stringr", "SummarizedExperiment", "sys", "timechange", "tinytex", "UCSC.utils", "VariantAnnotation", "vctrs", "viridisLite", "withr", "xfun", "XML", "xml2", "XVector", "yaml" ], "_vignettes": [ { "source": "bumphunterExample.Rmd", "filename": "bumphunterExample.html", "title": "Example report using bumphunter results", "author": "Leonardo Collado-Torres", "engine": "knitr::rmarkdown", "headings": [ "r Biocpkg('bumphunter') example", "Reproducibility" ], "created": "2015-07-01 11:47:42", "modified": "2025-07-27 00:59:40", "commits": 17 }, { "source": "regionReport.Rmd", "filename": "regionReport.html", "title": "Introduction to regionReport", "author": "Leonardo Collado-Torres", "engine": "knitr::rmarkdown", "headings": [ "Basics", "Install r Biocpkg('regionReport')", "Required knowledge", "Asking for help", "Citing r Biocpkg('regionReport')", "HTML reports for a set differential region results", "Using r Biocpkg('regionReport') for r Biocpkg('DESeq2') results", "Example", "Using r Biocpkg('regionReport') for r Biocpkg('edgeR') results", "Using r Biocpkg('regionReport') for region results", "Examples", "General case", "r Biocpkg('derfinder') single base-level case", "Run r Biocpkg('derfinder')", "Create report", "Notes", "Reproducibility", "Bibliography" ], "created": "2014-09-24 03:21:00", "modified": "2025-01-14 15:31:45", "commits": 50 } ], "_score": 7.272305844402086, "_indexed": false, "_nocasepkg": "regionreport", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/regionReport", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.46.0", "date": "2026-05-31T06:49:10.000Z", "distro": "noble", "commit": "0b5727526bcfef664522bde1f681ce5ee2add101", "fileid": "c4367f278e3253ed43d736f9395231a71c11208a88abfecdb37c303bd9f1af35", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26705532136" }, { "r": "4.6.0", "os": "linux", "version": "1.46.0", "date": "2026-05-31T06:49:11.000Z", "distro": "noble", "commit": "0b5727526bcfef664522bde1f681ce5ee2add101", "fileid": "bc5b8fc78f8df538df8f631e9a7224d5be021be253f1088b5bfeeebb023fe573", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26705532136" }, { "r": "4.5.3", "os": "mac", "version": "1.46.0", "date": "2026-05-31T07:48:29.000Z", "commit": "0b5727526bcfef664522bde1f681ce5ee2add101", "fileid": "85627ebfd33f2e3ff237bffbe37b274a6ba7871fba18c869ae6062d34112b4e6", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26705532136" }, { "r": "4.6.0", "os": "mac", "version": "1.46.0", "date": "2026-05-31T07:48:42.000Z", "commit": "0b5727526bcfef664522bde1f681ce5ee2add101", "fileid": "aeee10bc9b7a10929d354afe3c608b714847ad54b41ee7edd13569efeb045690", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26705532136" }, { "r": "4.6.0", "os": "wasm", "version": "1.46.0", "date": "2026-05-31T06:48:33.000Z", "commit": "0b5727526bcfef664522bde1f681ce5ee2add101", "fileid": "0bbecaed4ebcf98e47a47af4610c3454bb8533963ced8cf95fedbac3fc4b24a8", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26705532136" }, { "r": "4.7.0", "os": "win", "version": "1.46.0", "date": "2026-05-31T06:50:09.000Z", "commit": "0b5727526bcfef664522bde1f681ce5ee2add101", "fileid": "30389653d5efa089325781b3c54db1aea223c16ebc7a4bf7f2aab794e4b5877d", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26705532136" }, { "r": "4.5.3", "os": "win", "version": "1.46.0", "date": "2026-05-31T06:48:48.000Z", "commit": "0b5727526bcfef664522bde1f681ce5ee2add101", "fileid": "a85624e19f42424c6e001552bf3190996a387e1b5cfbf58362bafbf80497bd7b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26705532136" }, { "r": "4.6.0", "os": "win", "version": "1.46.0", "date": "2026-05-31T06:49:52.000Z", "commit": "0b5727526bcfef664522bde1f681ce5ee2add101", "fileid": "a0b8d402f9c8e128f9233e3e493fee62a13399556168d8b8ac34c40fb4f9a440", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26705532136" } ] }