{ "_id": "6a366b4f3efcd9bda4408fe9", "Package": "bamsignals", "Type": "Package", "Title": "Extract read count signals from bam files", "Version": "1.44.1", "Date": "2026-05-21", "Authors@R": "c( person(given=\"Alessandro\",family=\"Mammana\",\nemail=\"mammana@molgen.mpg.de\", role=c(\"aut\", \"cre\")),\nperson(given=\"Johannes\",family=\"Helmuth\",\nemail=\"johannes.helmuth@laborberlin.com\", role=c(\"aut\")))", "Author": "Alessandro Mammana [aut, cre], Johannes Helmuth [aut]", "Maintainer": "Johannes Helmuth ", "Description": "This package allows to efficiently obtain count vectors\nfrom indexed bam files. It counts the number of reads in given\ngenomic ranges and it computes reads profiles and coverage\nprofiles. It also handles paired-end data.", "License": "GPL-2", "SystemRequirements": "GNU make", "biocViews": "DataImport, Sequencing, Coverage, Alignment", "VignetteBuilder": "knitr", "NeedsCompilation": "yes", "RoxygenNote": "5.0.1", "URL": "https://github.com/lamortenera/bamsignals", "BugReports": "https://github.com/lamortenera/bamsignals/issues", "Config/pak/sysreqs": "make libbz2-dev liblzma-dev xz-utils zlib1g-dev", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-05-21 15:32:16 UTC", "RemoteUrl": "https://github.com/bioc/bamsignals", "RemoteRef": "RELEASE_3_23", "RemoteSha": "f9cc665ac686a6f7dca0e909fe9e3c54c7840db7", "Packaged": { "Date": "2026-06-20 10:21:29 UTC", "User": "root" }, "MD5sum": "ee5a8f7a18203ba16634114159673fe4", "_user": "bioc-release", "_type": "src", "_file": "bamsignals_1.44.1.tar.gz", "_fileid": "8a9fc42ac729e61ce2bfb774d0cf1b994735c387b383c0252296c8d687a9077d", "_filesize": 3348271, "_sha256": "8a9fc42ac729e61ce2bfb774d0cf1b994735c387b383c0252296c8d687a9077d", "_created": "2026-06-20T10:21:29.000Z", "_published": "2026-06-20T10:28:31.712Z", "_jobs": [ { "job": 82475813845, "time": 171, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7764497412" }, { "job": 82475813862, "time": 191, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "7764500183" }, { "job": 82475813856, "time": 198, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7764500678" }, { "job": 82475813863, "time": 208, "config": "linux-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7764502122" }, { "job": 82475813869, "time": 241, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7764505547" }, { "job": 82475813865, "time": 117, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7764491017" }, { "job": 82475813851, "time": 369, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "7764519035" }, { "job": 82475813854, "time": 125, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7764492090" }, { "job": 82475813850, "time": 214, "config": "macos-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7764502366" }, { "job": 82475583501, "time": 235, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7764476934" }, { "job": 82475813829, "time": 143, "config": "wasm-release", "r": "4.6.0", "check": "FAIL", "artifact": "" }, { "job": 82475813871, "time": 265, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7764508302" }, { "job": 82475813840, "time": 222, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7764503324" }, { "job": 82475813844, "time": 220, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7764503070" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 8 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27868155163", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/bamsignals", "_commit": { "id": "f9cc665ac686a6f7dca0e909fe9e3c54c7840db7", "author": "your-highness ", "committer": "your-highness ", "message": "Version bump to 1.44.1\n", "time": 1779377536 }, "_maintainer": { "name": "Johannes Helmuth", "email": "johannes.helmuth@laborberlin.com", "login": "your-highness", "mastodon": "@hoellenmotte@genomic.social", "linkedin": "in/johanneshelmuth", "description": "Bioinformatician in Clinical Diagnostics @LaborBerlin \n| PhD in Computational Epigenomics | Free Software Enthusiast for Audio Production ", "uuid": 1949888 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "Rhtslib", "version": ">= 1.13.1", "role": "LinkingTo" }, { "package": "methods", "role": "Imports" }, { "package": "BiocGenerics", "role": "Imports" }, { "package": "Rcpp", "version": ">= 0.10.6", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "GenomicRanges", "role": "Imports" }, { "package": "testthat", "version": ">= 0.9", "role": "Suggests" }, { "package": "Rsamtools", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 9, "_updates": [ { "week": "2026-21", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.45.1", "bioc": "3.24" }, { "branch": "release", "version": "1.44.1", "bioc": "3.23" } ], "_topics": [ "dataimport", "sequencing", "coverage", "alignment", "curl", "bzip2", "xz-utils", "zlib", "cpp" ], "_stars": 15, "_contributors": [ { "user": "your-highness", "count": 18, "uuid": 1949888 }, { "user": "lamortenera", "count": 16, "uuid": 327763 }, { "user": "jwokaty", "count": 16, "uuid": 1744257 }, { "user": "nturaga", "count": 14, "uuid": 2746443 }, { "user": "dtenenba", "count": 11, "uuid": 2286826 }, { "user": "hpages", "count": 7, "uuid": 8810451 }, { "user": "nhayden", "count": 4, "uuid": 6475155 }, { "user": "vobencha", "count": 2, "uuid": 2466173 }, { "user": "link-ny", "count": 1, "uuid": 4392950 }, { "user": "sonali-bioc", "count": 1, "uuid": 6373953 }, { "user": "lshep", "count": 1, "uuid": 18724380 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 440, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_mentions": 5, "_devurl": "https://github.com/lamortenera/bamsignals", "_searchresults": 58, "_rbuild": "4.6.0", "_assets": [ "extra/bamsignals.html", "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", "manual.pdf" ], "_homeurl": "https://github.com/lamortenera/bamsignals", "_realowner": "bioc", "_cranurl": false, "_exports": [ "alignSignals", "as.list", "bamCount", "bamCoverage", "bamProfile", "width" ], "_help": [ { "page": "as.list.CountSignals", "title": "Converts the container to a list 'l' such that 'l[[i]]' is the i-th signal.", "topics": [ "as.list.CountSignals" ] }, { "page": "bamsignals", "title": "Efficient counting of reads in a bam file", "topics": [ "bamsignals-package", "bamsignals" ] }, { "page": "bamsignals-methods", "title": "Functions for extracting count signals from a bam file.", "topics": [ "bamCount", "bamCount,character,GenomicRanges-method", "bamCoverage", "bamCoverage,character,GenomicRanges-method", "bamProfile", "bamProfile,character,GenomicRanges-method", "bamsignals-methods" ] }, { "page": "CountSignals-class", "title": "Container for count signals", "topics": [ "alignSignals", "alignSignals,CountSignals-method", "as.list", "as.list,CountSignals-method", "CountSignals", "CountSignals-class", "length", "length,CountSignals-method", "width", "width,CountSignals-method", "[,CountSignals,ANY-method" ] } ], "_readme": "https://github.com/bioc/bamsignals/raw/RELEASE_3_23/README.md", "_rundeps": [ "BiocGenerics", "generics", "GenomicRanges", "IRanges", "Rcpp", "Rhtslib", "S4Vectors", "Seqinfo" ], "_sysdeps": [ { "shlib": "libcurl", "package": "libcurl4t64", "headers": "libcurl4-openssl-dev", "source": "curl", "version": "8.5.0-2ubuntu10.9", "name": "curl", "homepage": "https://curl.se/", "description": "easy-to-use client-side URL transfer library (OpenSSL flavour)" }, { "shlib": "libbz2", "package": "libbz2-1.0", "headers": "libbz2-dev", "source": "bzip2", "version": "1.0.8-5.1build0.1", "name": "bzip2", "homepage": "https://sourceware.org/bzip2/", "description": "high-quality block-sorting file compressor library - runtime" }, { "shlib": "liblzma", "package": "liblzma5", "headers": "liblzma-dev", "source": "xz-utils", "version": "5.6.1+really5.4.5-1ubuntu0.3", "name": "xz-utils", "homepage": "https://tukaani.org/xz/", "description": "XZ-format compression library" }, { "shlib": "libz", "package": "zlib1g", "headers": "zlib1g-dev", "source": "zlib", "version": "1:1.3.dfsg-3.1ubuntu2.1", "name": "zlib", "homepage": "http://zlib.net/", "description": "compression library - runtime" }, { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_vignettes": [ { "source": "bamsignals.Rmd", "filename": "bamsignals.html", "title": "Introduction to the bamsignals package", "author": "Alessandro Mammana and Johannes Helmuth", "engine": "knitr::rmarkdown", "headings": [ "Introduction to the bamsignals package", "Loading toy data", "Counting reads in given ranges with bamCount()", "Basic counting", "Accounting for fragment length", "Counting on each strand separately", "Read profiles for each region with bamProfile()", "Regions of the same width", "Binning counts", "Read coverage with bamCoverage()", "Advanced bamsignals filtering options", "Exclude ambiguous reads with the mapq argument", "Filter reads with the filteredFlag argument", "Paired End Data", "Paired end data handling with the paired.end argument", "Filtering fragments with the tlenFilter argument" ], "created": "2015-02-13 21:00:36", "modified": "2016-04-11 07:41:32", "commits": 11 } ], "_score": 8.768823025449644, "_indexed": false, "_nocasepkg": "bamsignals", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/bamsignals", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.44.1", "date": "2026-06-20T10:24:14.000Z", "distro": "noble", "arch": "aarch64", "commit": "f9cc665ac686a6f7dca0e909fe9e3c54c7840db7", "fileid": "a0eced0437b6b42973aa921538f382b54fe13cad9081360203c33c39c48268bf", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27868155163" }, { "r": "4.7.0", "os": "linux", "version": "1.44.1", "date": "2026-06-20T10:24:19.000Z", "distro": "noble", "arch": "x86_64", "commit": "f9cc665ac686a6f7dca0e909fe9e3c54c7840db7", "fileid": "c1ad9d2f559e86612c849d08a6da0f3b95de91ee64d073f6cd51fbfa441d0ee9", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27868155163" }, { "r": "4.6.0", "os": "linux", "version": "1.44.1", "date": "2026-06-20T10:24:35.000Z", "distro": "noble", "arch": "aarch64", "commit": "f9cc665ac686a6f7dca0e909fe9e3c54c7840db7", "fileid": "bc710d0e77a75ccab27093748f0a2003dd47808f63529b85e805c495b06d5c32", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27868155163" }, { "r": "4.6.0", "os": "linux", "version": "1.44.1", "date": "2026-06-20T10:24:58.000Z", "distro": "noble", "arch": "x86_64", "commit": "f9cc665ac686a6f7dca0e909fe9e3c54c7840db7", "fileid": "a02b80bbce3f165d615b1c9b742c19397befa195c1fe6d12ea987e9899ebe8d0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27868155163" }, { "r": "4.5.3", "os": "mac", "version": "1.44.1", "date": "2026-06-20T10:23:20.000Z", "arch": "aarch64", "commit": "f9cc665ac686a6f7dca0e909fe9e3c54c7840db7", "fileid": "95e66b8b745b24d691ab8144bf20b6c6fec95253ea7700f0f802db36ec3f3a11", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27868155163" }, { "r": "4.5.3", "os": "mac", "version": "1.44.1", "date": "2026-06-20T10:25:46.000Z", "arch": "x86_64", "commit": "f9cc665ac686a6f7dca0e909fe9e3c54c7840db7", "fileid": "7fea682fdfa31187ac66f153367053306132839896844f7ba003af0b7b202656", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27868155163" }, { "r": "4.6.0", "os": "mac", "version": "1.44.1", "date": "2026-06-20T10:23:22.000Z", "arch": "aarch64", "commit": "f9cc665ac686a6f7dca0e909fe9e3c54c7840db7", "fileid": "7ab30e542eab198e59a2bcf7d215d34634be171f24971c5fc60e38a7fb523769", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27868155163" }, { "r": "4.6.0", "os": "mac", "version": "1.44.1", "date": "2026-06-20T10:24:08.000Z", "arch": "x86_64", "commit": "f9cc665ac686a6f7dca0e909fe9e3c54c7840db7", "fileid": "dfdc1e1224c22ffc6c278be8697280f9b3e25bebc4aa9fef1d738c9608ed6cee", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27868155163" }, { "r": "4.7.0", "os": "win", "version": "1.44.1", "date": "2026-06-20T10:23:59.000Z", "arch": "x86_64", "commit": "f9cc665ac686a6f7dca0e909fe9e3c54c7840db7", "fileid": "46901b8b5e90c44e610e0ecbffaf9b709ee944d8f8f6db64d93cf76e915337d7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27868155163" }, { "r": "4.5.3", "os": "win", "version": "1.44.1", "date": "2026-06-20T10:23:16.000Z", "arch": "x86_64", "commit": "f9cc665ac686a6f7dca0e909fe9e3c54c7840db7", "fileid": "a1efcdb6a88e51b80793868cf553513d7582d8a2f4ae8657ac1b36c4199668ba", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27868155163" }, { "r": "4.6.0", "os": "win", "version": "1.44.1", "date": "2026-06-20T10:23:15.000Z", "arch": "x86_64", "commit": "f9cc665ac686a6f7dca0e909fe9e3c54c7840db7", "fileid": "e3050cdc4453df06b92c52bb56791f9d049491dd6ffb25ac2a107bbb1ebf10a8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27868155163" } ] }