{ "_id": "6a1f0e69b401979e7341d2f6", "Package": "bedr", "Type": "Package", "Title": "Genomic Region Processing using Tools Such as 'BEDTools',\n'BEDOPS' and 'Tabix'", "Version": "1.1.5", "Authors@R": "c(\nperson(\"Syed\", \"Haider\", role = \"aut\"),\nperson(\"Daryl\", \"Waggott\", role = \"aut\"),\nperson(\"Emilie\", \"Lalonde\", role = \"ctb\"),\nperson(\"Clement\", \"Fung\", role = \"ctb\"),\nperson(\"Helena\", \"Winata\", role = \"ctb\"),\nperson(\"Dan\", \"Knight\", role = \"ctb\"),\nperson(\"Michael\", \"Chirico\", role = \"ctb\"),\nperson(\"Melinda\", \"Luo\", role = \"ctb\"),\nperson(\"Paul\", \"C. Boutros\", role = c(\"aut\", \"cre\", \"cph\"), email = \"pboutros@sbpdiscovery.org\")\n)", "Description": "Genomic regions processing using open-source command line\ntools such as 'BEDTools', 'BEDOPS' and 'Tabix'. These tools\noffer scalable and efficient utilities to perform genome\narithmetic e.g indexing, formatting and merging. bedr API\nenhances access to these tools as well as offers additional\nutilities for genomic regions processing.", "SystemRequirements": "Preferred genomic operations engine: 'BEDTools',\n'BEDOPS' and 'Tabix (>= 1.3)'.", "VignetteBuilder": "knitr", "License": "GPL-2", "URL": "https://github.com/theboutroslab/package-bedr", "BugReports": "https://github.com/theboutroslab/package-bedr/issues", "Config/testthat/edition": "3", "Config/pak/sysreqs": "cmake make libuv1-dev", "Repository": "https://theboutroslab.r-universe.dev", "Date/Publication": "2026-03-18 22:27:01 UTC", "RemoteUrl": "https://github.com/theboutroslab/package-bedr", "RemoteRef": "HEAD", "RemoteSha": "a41049308b7146d881dce24cc0d221fb033366bb", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-17 08:54:48 UTC", "User": "root" }, "Author": "Syed Haider [aut],\nDaryl Waggott [aut],\nEmilie Lalonde [ctb],\nClement Fung [ctb],\nHelena Winata [ctb],\nDan Knight [ctb],\nMichael Chirico [ctb],\nMelinda Luo [ctb],\nPaul C. Boutros [aut, cre, cph]", "Maintainer": "Paul C. 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"bedr.join.multiple.region", "title": "join multiple region objects", "topics": [ "bedr.join.multiple.region" ] }, { "page": "bedr.join.region", "title": "join two region objects using a left outer join", "topics": [ "bedr.join.region" ] }, { "page": "bedr.merge.region", "title": "merge i.e. collapse overlpaping regions", "topics": [ "bedr.merge.region" ] }, { "page": "bedr.plot.region", "title": "Visualize regions or intervals", "topics": [ "bedr.plot.region" ] }, { "page": "bedr.setup", "title": "Initialize some config settings for bedr", "topics": [ "bedr.setup" ] }, { "page": "bedr.snm.region", "title": "sort a region file", "topics": [ "bedr.snm.region" ] }, { "page": "bedr.sort.region", "title": "sort a region file", "topics": [ "bedr.sort.region" ] }, { "page": "bedr.subtract.region", "title": "subtracts features or ranges in object b from object a", "topics": [ "bedr.subtract.region" ] }, { "page": "catv", "title": "outputs text if verbose flag is set", "topics": [ "catv" ] }, { "page": "check.binary", "title": "checks if binary is in the path", "topics": [ "check.binary" ] }, { "page": "cluster.region", "title": "cluster intervals", "topics": [ "cluster.region" ] }, { "page": "convert2bed", "title": "convert object to bed format", "topics": [ "convert2bed" ] }, { "page": "create.tmp.bed.file", "title": "output R objects as tmpfiles", "topics": [ "create.tmp.bed.file" ] }, { "page": "determine.input", "title": "Determine input format", "topics": [ "determine.input" ] }, { "page": "df2list", "title": "Data frame to list conversion", "topics": [ "df2list" ] }, { "page": "download.datasets", "title": "Download some useful datasets", "topics": [ "download.datasets" ] }, { "page": "flank.region", "title": "Get adjacent flanks from regions", "topics": [ "flank.region" ] }, { "page": "get.bedpe.id", "title": "get BEDPE ID from VCF ID", "topics": [ "get.bedpe.id" ] }, { "page": "get.chr.length", "title": "gets the length of each chromosome for a species/build", 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