{
  "_id": "6ae745339ceaa78f20099a7a",
  "Package": "bamsignals",
  "Type": "Package",
  "Title": "Extract read count signals from bam files",
  "Version": "1.45.1",
  "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 <johannes.helmuth@laborberlin.com>",
  "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.r-universe.dev",
  "Date/Publication": "2026-05-21 15:28:44 UTC",
  "RemoteUrl": "https://github.com/bioc/bamsignals",
  "RemoteRef": "HEAD",
  "RemoteSha": "80ce5c52a4249962c07c65a4871824e58dab5590",
  "Packaged": {
    "Date": "2026-11-01 12:55:54 UTC",
    "User": "root"
  },
  "_user": "bioc",
  "_type": "src",
  "_file": "bamsignals_1.45.1.tar.gz",
  "_fileid": "https://r2.ropensci.org/c9d1f5c0a8e07c8cb6063fd6f7fb1feb8e8661ff505dd196799ccc92132fd42f",
  "_filesize": 3344699,
  "_sha256": "c9d1f5c0a8e07c8cb6063fd6f7fb1feb8e8661ff505dd196799ccc92132fd42f",
  "_expires": "2027-02-09T13:57:05.000Z",
  "_created": "2026-11-01T12:55:54.000Z",
  "_published": "2026-11-01T13:57:07.141Z",
  "_upstream": "https://github.com/bioc/bamsignals",
  "_status": "success",
  "_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
  },
  "_jobs": [
    {
      "job": 124854798226,
      "time": 158,
      "config": "bioc-checks",
      "r": "4.6.2",
      "check": "NOTE",
      "artifact": "13084372702"
    },
    {
      "job": 124854798260,
      "time": 162,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "13084248674"
    },
    {
      "job": 124854798285,
      "time": 211,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "13084429104"
    },
    {
      "job": 124854798313,
      "time": 154,
      "config": "linux-release-arm64",
      "r": "4.6.2",
      "check": "OK",
      "artifact": "13084820463"
    },
    {
      "job": 124854798327,
      "time": 249,
      "config": "linux-release-x86_64",
      "r": "4.6.2",
      "check": "OK",
      "artifact": "13084901631"
    },
    {
      "job": 124854798257,
      "time": 128,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "13085143644"
    },
    {
      "job": 124854798286,
      "time": 412,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "13085193764"
    },
    {
      "job": 124854798299,
      "time": 153,
      "config": "macos-release-arm64",
      "r": "4.6.2",
      "check": "OK",
      "artifact": "13085347514"
    },
    {
      "job": 124854798276,
      "time": 272,
      "config": "macos-release-x86_64",
      "r": "4.6.2",
      "check": "OK",
      "artifact": "13084969165"
    },
    {
      "job": 124853802742,
      "time": 266,
      "config": "source",
      "r": "4.6.2",
      "check": "OK",
      "artifact": "13084346862"
    },
    {
      "job": 124854798232,
      "time": 156,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "13084497454"
    },
    {
      "job": 124854798288,
      "time": 255,
      "config": "windows-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "13084184058"
    },
    {
      "job": 124854798282,
      "time": 264,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "13084836850"
    },
    {
      "job": 124854798411,
      "time": 207,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "13085021137"
    },
    {
      "job": 124854798280,
      "time": 258,
      "config": "windows-release-arm64",
      "r": "4.6.2",
      "check": "OK",
      "artifact": "13083989891"
    },
    {
      "job": 124854798274,
      "time": 235,
      "config": "windows-release-x86_64",
      "r": "4.6.2",
      "check": "OK",
      "artifact": "13084821071"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 7
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/41308486325",
  "_commit": {
    "id": "80ce5c52a4249962c07c65a4871824e58dab5590",
    "author": "your-highness <johannes.helmuth@laborberlin.com>",
    "committer": "your-highness <johannes.helmuth@laborberlin.com>",
    "message": "Merge remote-tracking branch 'upstream/devel'\n",
    "time": 1779377324
  },
  "_distro": "resolute",
  "_host": "GitHub-Actions",
  "_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": true,
  "_usedby": 8,
  "_updates": [
    {
      "week": "2026-21",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.45.1",
      "bioc": "3.24",
      "repository": "bioc"
    },
    {
      "branch": "release",
      "version": "1.44.1",
      "bioc": "3.23",
      "repository": "bioc"
    }
  ],
  "_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": 482,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 2980,
    "source": "https://www.bioconductor.org/packages/stats/bioc/bamsignals"
  },
  "_mentions": 5,
  "_devurl": "https://github.com/lamortenera/bamsignals",
  "_searchresults": 63,
  "_abi": {
    "exports": [
      {
        "key": "bamsignals::CountSignals",
        "hash": "97236d9ba8a69275"
      },
      {
        "key": "bamsignals::generic:alignSignals",
        "hash": "c83e6af31aac88d0"
      },
      {
        "key": "bamsignals::generic:bamCount",
        "hash": "01521568be0613cf"
      },
      {
        "key": "bamsignals::generic:bamCoverage",
        "hash": "9f129a355a81c4f3"
      },
      {
        "key": "bamsignals::generic:bamProfile",
        "hash": "c2d0cb62aefcea08"
      }
    ],
    "imports": [
      {
        "key": "BiocGenerics::generic:width",
        "hash": "667b5cc67ec1c535"
      },
      {
        "key": "Rcpp::Rcpp_precious_preserve()",
        "hash": "33a97ea62b293da6"
      },
      {
        "key": "Rcpp::Rcpp_precious_remove()",
        "hash": "63d26947ba7e1377"
      },
      {
        "key": "Rcpp::dataptr()",
        "hash": "54e69ad2e6668c83"
      },
      {
        "key": "Rcpp::demangle()",
        "hash": "b0cfd6754c5ebc4e"
      },
      {
        "key": "Rcpp::enterRNGScope()",
        "hash": "a04a299137cef947"
      },
      {
        "key": "Rcpp::exitRNGScope()",
        "hash": "a04a299137cef947"
      },
      {
        "key": "Rcpp::rcpp_get_stack_trace()",
        "hash": "c684a9bbe15cdc52"
      },
      {
        "key": "Rcpp::rcpp_set_stack_trace()",
        "hash": "33a97ea62b293da6"
      }
    ]
  },
  "_rbuild": "4.6.2",
  "_assets": [
    "extra/bamsignals.html",
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md"
  ],
  "_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/HEAD/README.md",
  "_rundeps": [
    "BiocGenerics",
    "generics",
    "GenomicRanges",
    "IRanges",
    "Rcpp",
    "Rhtslib",
    "S4Vectors",
    "Seqinfo"
  ],
  "_sysdeps": [
    {
      "shlib": "libcurl",
      "package": "libcurl4t64",
      "headers": "libcurl4-openssl-dev",
      "source": "curl",
      "version": "8.18.0-1ubuntu2.8",
      "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": "1.0.8-6ubuntu0.1",
      "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": "5.8.3-1ubuntu0.1",
      "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+really1.3.1-1ubuntu3.2",
      "name": "zlib",
      "homepage": "http://zlib.net/",
      "description": "compression library - runtime"
    },
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "16-20260322-1ubuntu1",
      "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": 9.227799322969162,
  "_indexed": true,
  "_nocasepkg": "bamsignals",
  "_universes": [
    "bioc",
    "your-highness",
    "lamortenera"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.45.1",
      "date": "2026-11-01T12:59:09.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "80ce5c52a4249962c07c65a4871824e58dab5590",
      "fileid": "https://r2.ropensci.org/0c11622296020321a7f8d317016e8740d9b8bcbf2f009b690b6ec063eadb196a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41308486325"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.45.1",
      "date": "2026-11-01T13:04:09.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "80ce5c52a4249962c07c65a4871824e58dab5590",
      "fileid": "https://r2.ropensci.org/650c88cdf6e87496132f7c3cda3ae14160f57014ff174cdcca9162f397b1f88e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41308486325"
    },
    {
      "r": "4.6.2",
      "os": "linux",
      "version": "1.45.1",
      "date": "2026-11-01T12:59:13.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "80ce5c52a4249962c07c65a4871824e58dab5590",
      "fileid": "https://r2.ropensci.org/76626b1c9754be3cf5b3b77dbfac52345e6671f6169645df7dd8a39e011bccde",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41308486325"
    },
    {
      "r": "4.6.2",
      "os": "linux",
      "version": "1.45.1",
      "date": "2026-11-01T13:05:03.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "80ce5c52a4249962c07c65a4871824e58dab5590",
      "fileid": "https://r2.ropensci.org/fa28d6143f3d7efe2fdf7061d6d951645260fa54a70fde199ca4602eea8f8c72",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41308486325"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.45.1",
      "date": "2026-11-01T13:23:29.000Z",
      "arch": "aarch64",
      "commit": "80ce5c52a4249962c07c65a4871824e58dab5590",
      "fileid": "https://r2.ropensci.org/a972d1f8477aaca0a5e0656a464db98e3847b51fd5097c0c3390ef9886cb8c12",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41308486325"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.45.1",
      "date": "2026-11-01T13:23:14.000Z",
      "arch": "x86_64",
      "commit": "80ce5c52a4249962c07c65a4871824e58dab5590",
      "fileid": "https://r2.ropensci.org/7b6862318e8492dd14f766e3b8b3f1a0ea1dbb7dc6b74ba99202d43709b750b7",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41308486325"
    },
    {
      "r": "4.6.2",
      "os": "mac",
      "version": "1.45.1",
      "date": "2026-11-01T13:23:43.000Z",
      "arch": "aarch64",
      "commit": "80ce5c52a4249962c07c65a4871824e58dab5590",
      "fileid": "https://r2.ropensci.org/8d95f6f275de471de7a41f120ae67d4b8755574080b19a24d69fb7208d6beacf",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41308486325"
    },
    {
      "r": "4.6.2",
      "os": "mac",
      "version": "1.45.1",
      "date": "2026-11-01T13:21:47.000Z",
      "arch": "x86_64",
      "commit": "80ce5c52a4249962c07c65a4871824e58dab5590",
      "fileid": "https://r2.ropensci.org/a5108609e6f5c7307523745627d33141db54202ef1485404ac95672181fe79e3",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41308486325"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.45.1",
      "date": "2026-11-01T13:04:01.000Z",
      "arch": "emscripten",
      "commit": "80ce5c52a4249962c07c65a4871824e58dab5590",
      "fileid": "https://r2.ropensci.org/dc965a10e99c69a3a85e12e0bda7415f1aa653323b995ea40ec2588c8efad61e",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41308486325"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.45.1",
      "date": "2026-11-01T13:00:20.000Z",
      "arch": "aarch64",
      "commit": "80ce5c52a4249962c07c65a4871824e58dab5590",
      "fileid": "https://r2.ropensci.org/0f916313ce74d396e24811bad3d3123c552f09ab0e9b389061c01dfe541cc76d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41308486325"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.45.1",
      "date": "2026-11-01T13:02:56.000Z",
      "arch": "x86_64",
      "commit": "80ce5c52a4249962c07c65a4871824e58dab5590",
      "fileid": "https://r2.ropensci.org/e2528f5ec9e72bed3c1a0e8e19738ece0cdb84b5e457256c13057e01b7ff4bdb",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41308486325"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.45.1",
      "date": "2026-11-01T13:03:13.000Z",
      "arch": "x86_64",
      "commit": "80ce5c52a4249962c07c65a4871824e58dab5590",
      "fileid": "https://r2.ropensci.org/3f81e2635282c42b373017d17577dac3c92bf85456239c277a53c6a24941734c",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41308486325"
    },
    {
      "r": "4.6.2",
      "os": "win",
      "version": "1.45.1",
      "date": "2026-11-01T13:00:19.000Z",
      "arch": "aarch64",
      "commit": "80ce5c52a4249962c07c65a4871824e58dab5590",
      "fileid": "https://r2.ropensci.org/ca00bfcab6975eb309108baa5b96ce13d405a000f25675e0293958ca3cc29aec",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41308486325"
    },
    {
      "r": "4.6.2",
      "os": "win",
      "version": "1.45.1",
      "date": "2026-11-01T13:03:19.000Z",
      "arch": "x86_64",
      "commit": "80ce5c52a4249962c07c65a4871824e58dab5590",
      "fileid": "https://r2.ropensci.org/18f45c8404dcf2c7caab5ff7568ec8c49864abdbf0cc582b0a7cee215363ec7f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41308486325"
    }
  ]
}