{ "_id": "6a37c5583efcd9bda442e514", "Package": "megadepth", "Title": "megadepth: BigWig and BAM related utilities", "Version": "1.22.0", "Date": "2021-08-05", "Authors@R": "c(\nperson(\n\"Leonardo\", \"Collado-Torres\", role = c(\"aut\"),\nemail = \"lcolladotor@gmail.com\",\ncomment = c(ORCID = \"0000-0003-2140-308X\")\n),\nperson(\ngiven = \"David\",\nfamily = \"Zhang\",\nrole = c(\"aut\", \"cre\"),\nemail = \"david.zhang.12@ucl.ac.uk\",\ncomment = c(ORCID = \"0000-0003-2382-8460\")\n))", "Description": "This package provides an R interface to Megadepth by\nChristopher Wilks available at\nhttps://github.com/ChristopherWilks/megadepth. It is\nparticularly useful for computing the coverage of a set of\ngenomic regions across bigWig or BAM files. With this package,\nyou can build base-pair coverage matrices for regions or\nannotations of your choice from BigWig files. Megadepth was\nused to create the raw files provided by\nhttps://bioconductor.org/packages/recount3.", "License": "Artistic-2.0", "URL": "https://github.com/LieberInstitute/megadepth", "BugReports": "https://support.bioconductor.org/t/megadepth", "biocViews": "Software, Coverage, DataImport, Transcriptomics, RNASeq,\nPreprocessing", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.2.3", "SystemRequirements": "megadepth\n()", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Config/pak/sysreqs": "cmake git make libgit2-dev libuv1-dev libssl-dev\nlibx11-dev", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 12:54:14 UTC", "RemoteUrl": "https://github.com/bioc/megadepth", "RemoteRef": "RELEASE_3_23", "RemoteSha": "a02c700a7d02ae120a47be92359d3f284294936b", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-21 10:59:27 UTC", "User": "root" }, "Author": "Leonardo Collado-Torres [aut] (ORCID:\n),\nDavid Zhang [aut, cre] (ORCID: )", "Maintainer": "David Zhang ", "MD5sum": "462381fa767ba86fb747833728760fb5", "_user": "bioc-release", "_type": "src", "_file": "megadepth_1.22.0.tar.gz", "_fileid": "8f2e486d71bb81766264e0bc6caa80f67698d4547f14095008660eb5d5c96e66", "_filesize": 322897, "_sha256": "8f2e486d71bb81766264e0bc6caa80f67698d4547f14095008660eb5d5c96e66", "_created": "2026-06-21T10:59:27.000Z", "_published": "2026-06-21T11:04:56.696Z", "_jobs": [ { "job": 82564308560, "time": 198, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7774632786" }, { "job": 82564308567, "time": 296, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7774644281" }, { "job": 82564308587, "time": 258, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7774639863" }, { "job": 82564308579, "time": 147, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7774629202" }, { "job": 82564308586, "time": 154, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7774630446" }, { "job": 82564026859, "time": 279, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7774609120" }, { "job": 82564308571, "time": 180, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7774630562" }, { "job": 82564308602, "time": 154, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7774627299" }, { "job": 82564308603, "time": 165, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7774628821" }, { "job": 82564308593, "time": 168, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7774629220" } ], "_bioccheck": { "error": 0, "warning": 1, "note": 5 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27902059696", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/megadepth", "_commit": { "id": "a02c700a7d02ae120a47be92359d3f284294936b", "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": 1777380854 }, "_maintainer": { "name": "David Zhang", "email": "david.zhang.12@ucl.ac.uk", "orcid": "0000-0003-2382-8460" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "xfun", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "fs", "role": "Imports" }, { "package": "GenomicRanges", "role": "Imports" }, { "package": "readr", "role": "Imports" }, { "package": "cmdfun", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "magrittr", "role": "Imports" }, { "package": "covr", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "sessioninfo", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "rtracklayer", "role": "Suggests" }, { "package": "derfinder", "role": "Suggests" }, { "package": "GenomeInfoDb", "role": "Suggests" }, { "package": "tools", "role": "Suggests" }, { "package": "RefManageR", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 3, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-14", "n": 1 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.23.0", "bioc": "3.24" }, { "branch": "release", "version": "1.22.0", "bioc": "3.23" } ], "_topics": [ "software", "coverage", "dataimport", "transcriptomics", "rnaseq", "preprocessing", "bam", "bigwig", "daspter", "megadepth", "recount2", "recount3" ], "_stars": 14, "_contributors": [ { "user": "lcolladotor", "count": 94, "uuid": 2288213 }, { "user": "dzhang32", "count": 22, "uuid": 32676710 }, { "user": "jwokaty", "count": 14, "uuid": 1744257 }, { "user": "nturaga", "count": 8, "uuid": 2746443 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 440, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_mentions": 1, "_devurl": "https://github.com/lieberinstitute/megadepth", "_searchresults": 15, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/megadepth.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/lieberinstitute/megadepth", "_realowner": "bioc", "_cranurl": false, "_exports": [ "bam_to_bigwig", "bam_to_junctions", "get_coverage", "install_megadepth", "megadepth_cmd", "megadepth_shell", "process_junction_table", "read_coverage", "read_coverage_table", "read_junction_table" ], "_help": [ { "page": "bam_to_bigwig", "title": "Convert a BAM file to a BigWig", "topics": [ "bam_to_bigwig" ] }, { "page": "bam_to_junctions", "title": "Extract junctions from a BAM file", "topics": [ "bam_to_junctions" ] }, { "page": "get_coverage", "title": "Compute coverage summarizations across a set of regions", "concept": [ "Coverage functions" ], "topics": [ "get_coverage" ] }, { "page": "install_megadepth", "title": "Install Megadepth", "topics": [ "install_megadepth" ] }, { "page": "megadepth_cmd", "title": "Run Megadepth commands", "topics": [ "megadepth_cmd", "megadepth_shell" ] }, { "page": "process_junction_table", "title": "Process junctions into a STAR compatible format", "topics": [ "process_junction_table" ] }, { "page": "read_coverage", "title": "Read a coverage TSV file created by Megadepth", "concept": [ "Coverage functions" ], "topics": [ "read_coverage", "read_coverage_table" ] }, { "page": "read_junction_table", "title": "Read a junction TSV file created by Megadepth as a table", "topics": [ "read_junction_table" ] } ], "_readme": "https://github.com/bioc/megadepth/raw/RELEASE_3_23/README.md", "_rundeps": [ "askpass", "BiocGenerics", "bit", "bit64", "brio", "callr", "cli", "clipr", "cmdfun", "cpp11", "crayon", "credentials", "curl", "desc", "diffobj", "dplyr", "evaluate", "fs", "generics", "GenomicRanges", "gert", "gitcreds", "glue", "hms", "httr2", "ini", "IRanges", "jsonlite", "lifecycle", "magrittr", "openssl", "otel", "pillar", "pkgbuild", "pkgconfig", "pkgload", "praise", "prettyunits", "processx", "progress", "ps", "purrr", "R.methodsS3", "R.oo", "R.utils", "R6", "rappdirs", "readr", "rlang", "rprojroot", "rstudioapi", "S4Vectors", "Seqinfo", "sys", "testthat", "tibble", "tidyselect", "tzdb", "usethis", "utf8", "vctrs", "vroom", "waldo", "whisker", "withr", "xfun", "yaml", "zip" ], "_vignettes": [ { "source": "megadepth.Rmd", "filename": "megadepth.html", "title": "megadepth quick start guide", "author": "David Zhang, Leonardo Collado-Torres", "engine": "knitr::rmarkdown", "headings": [ "Basics", "Install megadepth", "Required knowledge", "Asking for help", "Citing megadepth", "Quick start", "Users guide", "Command interface", "BAM to bigWig", "Summarize coverage over regions", "BAM to junctions", "Teams involved", "Other related tools", "Reproducibility", "Bibliography" ], "created": "2020-09-17 13:46:50", "modified": "2024-12-12 21:38:33", "commits": 15 } ], "_score": 6.929674317948589, "_indexed": false, "_nocasepkg": "megadepth", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/megadepth", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.22.0", "date": "2026-06-21T11:03:32.000Z", "distro": "noble", "commit": "a02c700a7d02ae120a47be92359d3f284294936b", "fileid": "bb6da65fcfe43a54aad5cb91343f5996acd37824280a6eb52dd4863df523f75d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27902059696" }, { "r": "4.6.0", "os": "linux", "version": "1.22.0", "date": "2026-06-21T11:03:00.000Z", "distro": "noble", "commit": "a02c700a7d02ae120a47be92359d3f284294936b", "fileid": "8fb41667e24850aafe4580b7d6496492ecc60349c5fd3c003f0aa6b6488523e9", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27902059696" }, { "r": "4.5.3", "os": "mac", "version": "1.22.0", "date": "2026-06-21T11:01:27.000Z", "commit": "a02c700a7d02ae120a47be92359d3f284294936b", "fileid": "67a5d545d5296170d20ba3e4f6015192b8bdb46811ac808e0dda705f19aa5e82", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27902059696" }, { "r": "4.6.0", "os": "mac", "version": "1.22.0", "date": "2026-06-21T11:01:35.000Z", "commit": "a02c700a7d02ae120a47be92359d3f284294936b", "fileid": "3a2d66705d312d19247ec00f9a3c5fcc5987701b059468075e41299c1c6fbfb6", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27902059696" }, { "r": "4.6.0", "os": "wasm", "version": "1.22.0", "date": "2026-06-21T11:02:44.000Z", "commit": "a02c700a7d02ae120a47be92359d3f284294936b", "fileid": "d1f57061810c5c4f7a3949d8d91e51f11b85d76beb4ef145149890e47331bdf7", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27902059696" }, { "r": "4.7.0", "os": "win", "version": "1.22.0", "date": "2026-06-21T11:01:09.000Z", "commit": "a02c700a7d02ae120a47be92359d3f284294936b", "fileid": "f81f1d049b09ab1a7220202c3d6065d41c49a17e11324cee5180c705115bf172", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27902059696" }, { "r": "4.5.3", "os": "win", "version": "1.22.0", "date": "2026-06-21T11:01:19.000Z", "commit": "a02c700a7d02ae120a47be92359d3f284294936b", "fileid": "4fb4706796f024bbae315d4e0198880be981a971c042f9737e7ac3afb1ada724", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27902059696" }, { "r": "4.6.0", "os": "win", "version": "1.22.0", "date": "2026-06-21T11:01:12.000Z", "commit": "a02c700a7d02ae120a47be92359d3f284294936b", "fileid": "e7ca368cddfa44692a9a346911dbcb260700d57cc9454adc98d05fb1a5f49533", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27902059696" } ] }