{ "_id": "6a494ba8f6c47c441949918f", "Package": "regionReport", "Type": "Package", "Title": "Generate HTML or PDF reports for a set of genomic regions or\nDESeq2/edgeR results", "Version": "1.47.0", "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.r-universe.dev", "Date/Publication": "2026-04-28 12:39:52 UTC", "RemoteUrl": "https://github.com/bioc/regionReport", "RemoteRef": "HEAD", "RemoteSha": "62a3b7a18204e33c2741b841ade871376ef798af", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-03 18:21:38 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 ", "_user": "bioc", "_type": "src", "_file": "regionReport_1.47.0.tar.gz", "_fileid": "https://r2.ropensci.org/5b99c5f6dd45434723a438bba6fe5df30ff9a596a4172f0b45cbf1ca34320bf1", "_filesize": 236493, "_sha256": "5b99c5f6dd45434723a438bba6fe5df30ff9a596a4172f0b45cbf1ca34320bf1", "_expires": "2026-10-12T18:06:30.000Z", "_created": "2026-07-03T18:21:38.000Z", "_published": "2026-07-04T18:06:32.092Z", "_bioccheck": { "error": 0, "warning": 0, "note": 7 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28677040481", "_status": "success", "_upstream": "https://github.com/bioc/regionReport", "_commit": { "id": "62a3b7a18204e33c2741b841ade871376ef798af", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following 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": "resolute", "_jobs": [ { "job": 85154826748, "time": 295, "config": "bioc-checks", "r": "4.6.1", "check": "NOTE", "artifact": "8072876024" }, { "job": 85154826724, "time": 758, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "8072976562" }, { "job": 85154826819, "time": 780, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "8072981298" }, { "job": 85154826706, "time": 456, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "8072911221" }, { "job": 85154826713, "time": 409, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "8072900268" }, { "job": 85154826445, "time": 379, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8072816224" }, { "job": 85154826812, "time": 269, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8072870365" }, { "job": 85154826709, "time": 773, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "8072979930" }, { "job": 85154826956, "time": 788, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "8072983568" }, { "job": 85154826804, "time": 782, "config": "windows-release", "r": "4.6.1", "check": "NOTE", "artifact": "8072981936" } ], "_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": true, "_usedby": 0, "_updates": [ { "week": "2025-30", "n": 2 }, { "week": "2025-44", "n": 2 }, { "week": "2026-14", "n": 1 }, { "week": "2026-18", "n": 2 } ], "_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", "followers": 445, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_mentions": 2, "_devurl": "https://github.com/leekgroup/regionreport", "_searchresults": 49, "_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/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/HEAD/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": 7.246498580795801, "_indexed": true, "_nocasepkg": "regionreport", "_universes": [ "bioc", "lcolladotor", "leekgroup" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.47.0", "date": "2026-07-03T18:27:10.000Z", "distro": "resolute", "commit": "62a3b7a18204e33c2741b841ade871376ef798af", "fileid": "https://r2.ropensci.org/5e87169100b1e3a4126f50fe228f252e53da9b9190467ea15bee2c392700285f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28677040481" }, { "r": "4.6.1", "os": "linux", "version": "1.47.0", "date": "2026-07-03T18:27:16.000Z", "distro": "resolute", "commit": "62a3b7a18204e33c2741b841ade871376ef798af", "fileid": "https://r2.ropensci.org/367222b60d51b91bb7746292daf7737b943378736749e0d71a5a411f7a1c592d", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28677040481" }, { "r": "4.5.3", "os": "mac", "version": "1.47.0", "date": "2026-07-03T18:24:22.000Z", "commit": "62a3b7a18204e33c2741b841ade871376ef798af", "fileid": "https://r2.ropensci.org/9d4ffaceb813786fa4ebadbd02cfdef9c4e9e44e44b5073adcdc10ab3167c194", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28677040481" }, { "r": "4.6.1", "os": "mac", "version": "1.47.0", "date": "2026-07-03T18:24:17.000Z", "commit": "62a3b7a18204e33c2741b841ade871376ef798af", "fileid": "https://r2.ropensci.org/e259fc34d3417361ac5e3e17c7cf507a62f85794efc7f9e2daf2cc965bf497f4", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28677040481" }, { "r": "4.6.0", "os": "wasm", "version": "1.47.0", "date": "2026-07-03T18:26:52.000Z", "commit": "62a3b7a18204e33c2741b841ade871376ef798af", "fileid": "https://r2.ropensci.org/41378629584228148e6fbbfcb1d711523be402081d7ffc0ba6d734e3242a0718", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28677040481" }, { "r": "4.7.0", "os": "win", "version": "1.47.0", "date": "2026-07-03T18:26:48.000Z", "commit": "62a3b7a18204e33c2741b841ade871376ef798af", "fileid": "https://r2.ropensci.org/b4e3c4ac2de49c1fa67137e553308e8e9b1f422409e51a7001db21abc945c02b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28677040481" }, { "r": "4.5.3", "os": "win", "version": "1.47.0", "date": "2026-07-03T18:27:15.000Z", "commit": "62a3b7a18204e33c2741b841ade871376ef798af", "fileid": "https://r2.ropensci.org/4d0301754e663db7e33f270deebff53e1d60d8a16604083a1baddc458a753793", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28677040481" }, { "r": "4.6.1", "os": "win", "version": "1.47.0", "date": "2026-07-03T18:26:55.000Z", "commit": "62a3b7a18204e33c2741b841ade871376ef798af", "fileid": "https://r2.ropensci.org/2843e031f540aa5492f788f95c8ad86dd8d8f96fc0b092bc1753c897478ffa4f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28677040481" } ] }