{
  "_id": "6ada928edd3792e773238b1a",
  "Package": "betterChromVAR",
  "Title": "Improved ChromVAR (Chromatin Variation Across Regions)",
  "Description": "A much faster analytical implementation of chromVAR, with\nadditional features, used to infer TF activity from (bulk or\nsingle-cell) ATAC-seq data and motif annotations (or binding\nprobabilities). The package also includes the CVnorm\nnormalization method based on the chromVAR logic.",
  "Version": "1.1.12",
  "Authors@R": "person(\"Pierre-Luc\", \"Germain\", email=\"pierre-luc.germain@hest.ethz.ch\", role=c(\"aut\",\"cre\"),\ncomment=c(ORCID=\"0000-0003-3418-4218\"))",
  "License": "GPL (>= 3)",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "URL": "https://github.com/plger/betterChromVAR",
  "BugReports": "https://github.com/plger/betterChromVAR/issues",
  "biocViews": "Software, ATACSeq, Normalization, Epigenetics, Sequencing",
  "Config/testthat/edition": "3",
  "VignetteBuilder": "knitr",
  "Config/roxygen2/version": "8.0.0",
  "Config/pak/sysreqs": "zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-10-19 09:23:34 UTC",
  "RemoteUrl": "https://github.com/bioc/betterChromVAR",
  "RemoteRef": "HEAD",
  "RemoteSha": "d64e3b5d0f52fa449c248be5e59010c8055da9ec",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-22 22:37:44 UTC",
    "User": "root"
  },
  "Author": "Pierre-Luc Germain [aut, cre] (ORCID:\n<https://orcid.org/0000-0003-3418-4218>)",
  "Maintainer": "Pierre-Luc Germain <pierre-luc.germain@hest.ethz.ch>",
  "_user": "bioc",
  "_type": "src",
  "_file": "betterChromVAR_1.1.12.tar.gz",
  "_fileid": "https://r2.ropensci.org/2a332ff09fcfe3bf137184705704f6789f5ea75f5f473810572dfe7741a3f2d8",
  "_filesize": 262679,
  "_sha256": "2a332ff09fcfe3bf137184705704f6789f5ea75f5f473810572dfe7741a3f2d8",
  "_expires": "2027-01-30T22:47:40.000Z",
  "_created": "2026-10-22T22:37:44.000Z",
  "_published": "2026-10-22T22:47:42.433Z",
  "_upstream": "https://github.com/bioc/betterChromVAR",
  "_status": "success",
  "_maintainer": {
    "name": "Pierre-Luc Germain",
    "email": "pierre-luc.germain@hest.ethz.ch",
    "login": "plger",
    "orcid": "0000-0003-3418-4218",
    "description": "like sailors who on the open sea must reconstruct their ship but are never able to start afresh from the bottom...",
    "uuid": 9786697
  },
  "_jobs": [
    {
      "job": 120129564016,
      "time": 333,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "12464232362"
    },
    {
      "job": 120129563956,
      "time": 460,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "12464681521"
    },
    {
      "job": 120129564118,
      "time": 535,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "12464976040"
    },
    {
      "job": 120129564072,
      "time": 212,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "12464491191"
    },
    {
      "job": 120129563944,
      "time": 265,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "12464855444"
    },
    {
      "job": 120127257448,
      "time": 347,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12463394576"
    },
    {
      "job": 120129563877,
      "time": 213,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "12463518790"
    },
    {
      "job": 120129564063,
      "time": 273,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "12463873130"
    },
    {
      "job": 120129563965,
      "time": 264,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "12464022641"
    },
    {
      "job": 120129564018,
      "time": 542,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "12465265167"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 8
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/39865673746",
  "_commit": {
    "id": "d64e3b5d0f52fa449c248be5e59010c8055da9ec",
    "author": "Pierre-Luc <pl.germain@gmail.com>",
    "committer": "GitHub <noreply@github.com>",
    "message": "Merge pull request #5 from plger/fpc\n\nMerge FPC into main/devel",
    "time": 1792401814
  },
  "_distro": "resolute",
  "_host": "GitHub-Actions",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.1.0",
      "role": "Depends"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Depends"
    },
    {
      "package": "BiocParallel",
      "role": "Imports"
    },
    {
      "package": "BiocNeighbors",
      "role": "Imports"
    },
    {
      "package": "Biostrings",
      "role": "Imports"
    },
    {
      "package": "DelayedMatrixStats",
      "role": "Imports"
    },
    {
      "package": "GenomicRanges",
      "role": "Imports"
    },
    {
      "package": "IRanges",
      "role": "Imports"
    },
    {
      "package": "Matrix",
      "role": "Imports"
    },
    {
      "package": "matrixStats",
      "role": "Imports"
    },
    {
      "package": "sparseMatrixStats",
      "role": "Imports"
    },
    {
      "package": "MatrixGenerics",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "sessioninfo",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-12",
      "n": 32
    },
    {
      "week": "2026-13",
      "n": 10
    },
    {
      "week": "2026-14",
      "n": 11
    },
    {
      "week": "2026-15",
      "n": 15
    },
    {
      "week": "2026-16",
      "n": 8
    },
    {
      "week": "2026-17",
      "n": 4
    },
    {
      "week": "2026-18",
      "n": 2
    },
    {
      "week": "2026-19",
      "n": 13
    },
    {
      "week": "2026-20",
      "n": 2
    },
    {
      "week": "2026-25",
      "n": 7
    },
    {
      "week": "2026-28",
      "n": 2
    },
    {
      "week": "2026-33",
      "n": 1
    },
    {
      "week": "2026-34",
      "n": 1
    },
    {
      "week": "2026-35",
      "n": 4
    },
    {
      "week": "2026-43",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.1.10",
      "bioc": "3.24",
      "repository": "bioc"
    },
    {
      "branch": "release",
      "version": "1.0.3",
      "bioc": "3.23",
      "repository": "bioc"
    }
  ],
  "_topics": [
    "software",
    "atacseq",
    "normalization",
    "epigenetics",
    "sequencing"
  ],
  "_stars": 2,
  "_contributors": [
    {
      "user": "plger",
      "count": 143,
      "uuid": 9786697
    },
    {
      "user": "jwokaty",
      "count": 2,
      "uuid": 1744257
    },
    {
      "user": "koefoeden",
      "count": 2,
      "uuid": 53121948
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 479,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 377,
    "source": "https://www.bioconductor.org/packages/stats/bioc/betterChromVAR"
  },
  "_devurl": "https://github.com/plger/betterchromvar",
  "_searchresults": 33,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/betterChromVAR.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/plger/betterchromvar",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "addGCBias",
    "betterChromVAR",
    "computeBackgrounds",
    "computeDeviationsAnalytic",
    "computeDeviationsFromKNN",
    "computeDeviationsWeighted",
    "computeMotifReliability",
    "computeMotifVariability",
    "CVnorm",
    "estimateNoiseKappa",
    "getBackgroundBins",
    "getBackgroundKNN",
    "getDummyData",
    "getExpectation",
    "normalizeDevsForSize",
    "sampleBackgroundPeaks",
    "show",
    "shrinkColumnProps",
    "smoothDeviationsKNN"
  ],
  "_help": [
    {
      "page": "addGCBias",
      "title": "addGCBias",
      "topics": [
        "addGCBias"
      ]
    },
    {
      "page": "bcvBackground-methods",
      "title": "Coerce bcvBackground to a list",
      "topics": [
        "as.list,bcvBackground-method",
        "show,bcvBackground-method",
        "[,bcvBackground,ANY,ANY,ANY-method"
      ]
    },
    {
      "page": "bcvBackground-class",
      "title": "Bin and background data for betterChromVAR (for internal use)",
      "topics": [
        "bcvBackground-class"
      ]
    },
    {
      "page": "betterChromVAR",
      "title": "betterChromVAR",
      "topics": [
        "betterChromVAR"
      ]
    },
    {
      "page": "computeBackgrounds",
      "title": "computeBackgrounds",
      "topics": [
        "computeBackgrounds"
      ]
    },
    {
      "page": "computeDeviationsAnalytic",
      "title": "computeDeviationsAnalytic",
      "topics": [
        "computeDeviationsAnalytic"
      ]
    },
    {
      "page": "computeDeviationsFromKNN",
      "title": "computeDeviationsFromKNNbg",
      "topics": [
        "computeDeviationsFromKNN"
      ]
    },
    {
      "page": "computeDeviationsWeighted",
      "title": "computeDeviationsWeighted",
      "topics": [
        "computeDeviationsWeighted"
      ]
    },
    {
      "page": "computeMotifReliability",
      "title": "computeMotifReliability",
      "topics": [
        "computeMotifReliability"
      ]
    },
    {
      "page": "computeMotifVariability",
      "title": "computeMotifVariability",
      "topics": [
        "computeMotifVariability"
      ]
    },
    {
      "page": "CVnorm",
      "title": "CVnorm: chromVAR-inspired ATAC-seq normalization",
      "topics": [
        "CVnorm"
      ]
    },
    {
      "page": "estimateNoiseKappa",
      "title": "estimateNoiseKappa",
      "topics": [
        "estimateNoiseKappa"
      ]
    },
    {
      "page": "getBackgroundBins",
      "title": "getBackgroundBins",
      "topics": [
        "getBackgroundBins"
      ]
    },
    {
      "page": "getBackgroundKNN",
      "title": "getBackgroundKNN",
      "topics": [
        "getBackgroundKNN"
      ]
    },
    {
      "page": "getDummyData",
      "title": "Dummy data for testing purposes",
      "topics": [
        "getDummyData"
      ]
    },
    {
      "page": "getExpectation",
      "title": "getExpectation",
      "topics": [
        "getExpectation"
      ]
    },
    {
      "page": "normalizeDevsForSize",
      "title": "normalizeDevsForSize",
      "topics": [
        "normalizeDevsForSize"
      ]
    },
    {
      "page": "sampleBackgroundPeaks",
      "title": "sampleBackgroundPeaks",
      "topics": [
        "sampleBackgroundPeaks"
      ]
    },
    {
      "page": "shrinkColumnProps",
      "title": "shrinkColumnProps",
      "topics": [
        "shrinkColumnProps"
      ]
    },
    {
      "page": "smoothDeviationsKNN",
      "title": "smoothDeviationsKNN",
      "topics": [
        "smoothDeviationsKNN"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/betterChromVAR/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "assorthead",
    "beachmat",
    "BH",
    "Biobase",
    "BiocGenerics",
    "BiocNeighbors",
    "BiocParallel",
    "Biostrings",
    "codetools",
    "cpp11",
    "crayon",
    "DelayedArray",
    "DelayedMatrixStats",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicRanges",
    "IRanges",
    "lambda.r",
    "lattice",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "Rcpp",
    "S4Arrays",
    "S4Vectors",
    "Seqinfo",
    "snow",
    "SparseArray",
    "sparseMatrixStats",
    "SummarizedExperiment",
    "XVector"
  ],
  "_vignettes": [
    {
      "source": "betterChromVAR.Rmd",
      "filename": "betterChromVAR.html",
      "title": "Introduction to betterChromVAR",
      "author": "Pierre-Luc Germain",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Installing betterChromVAR",
        "Computing motif deviations with betterChromVAR",
        "Individual steps of betterChromVAR",
        "Including fragment length bias",
        "Note on single-cell data",
        "Execution on Atlas-scale datasets",
        "Motif variability and reliability",
        "Smoothing the deviations of single cells across neighboring cells",
        "Bias-normalization of bulk ATAC-seq data",
        "betterChromVAR with kNN-based background",
        "Appendix",
        "References",
        "Session info"
      ],
      "created": "2026-03-17 13:31:26",
      "modified": "2026-10-19 09:23:34",
      "commits": 21
    }
  ],
  "_score": 5.99563519459755,
  "_indexed": true,
  "_nocasepkg": "betterchromvar",
  "_universes": [
    "bioc",
    "plger"
  ],
  "_previous": "1.1.10",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.1.12",
      "date": "2026-10-22T22:43:36.000Z",
      "distro": "resolute",
      "commit": "d64e3b5d0f52fa449c248be5e59010c8055da9ec",
      "fileid": "https://r2.ropensci.org/c6d6cfebb0c9dbf9104ae563608f5bd68bb0b7c1073ed067fca6eaa168e32e44",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39865673746"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.1.12",
      "date": "2026-10-22T22:44:09.000Z",
      "distro": "resolute",
      "commit": "d64e3b5d0f52fa449c248be5e59010c8055da9ec",
      "fileid": "https://r2.ropensci.org/1604207c01f577ab43a917b30240fa27a90393463c89ba1c4f33f5015321598c",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39865673746"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.1.12",
      "date": "2026-10-22T22:39:45.000Z",
      "commit": "d64e3b5d0f52fa449c248be5e59010c8055da9ec",
      "fileid": "https://r2.ropensci.org/178e9906f1a889e4e7ff277ef9727933ff30c419ce384737e0ff0bb0facf14a8",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39865673746"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.1.12",
      "date": "2026-10-22T22:39:59.000Z",
      "commit": "d64e3b5d0f52fa449c248be5e59010c8055da9ec",
      "fileid": "https://r2.ropensci.org/a41501bef4536355c50af774ae72d15312fefecf4f19a0994150c00fd9b9d29e",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39865673746"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.1.12",
      "date": "2026-10-22T22:41:48.000Z",
      "commit": "d64e3b5d0f52fa449c248be5e59010c8055da9ec",
      "fileid": "https://r2.ropensci.org/6acde9966a99dc37934eecbaf26c58d5d233076181753d67e3154538ce831813",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39865673746"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.1.12",
      "date": "2026-10-22T22:39:24.000Z",
      "commit": "d64e3b5d0f52fa449c248be5e59010c8055da9ec",
      "fileid": "https://r2.ropensci.org/c485cb1df9b80a40bf57bc98d50b2d2c7d0aa39ba5bc04d4cf85e20ace479414",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39865673746"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.1.12",
      "date": "2026-10-22T22:39:24.000Z",
      "commit": "d64e3b5d0f52fa449c248be5e59010c8055da9ec",
      "fileid": "https://r2.ropensci.org/631aa8c27c696bad27021632b2f2629c2a3dca1b4c832465a58d5552513ed9c8",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39865673746"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.1.12",
      "date": "2026-10-22T22:43:43.000Z",
      "commit": "d64e3b5d0f52fa449c248be5e59010c8055da9ec",
      "fileid": "https://r2.ropensci.org/6b62b1041656db6a85443888cb176a0f1ffee8d7a2d7e9ac90dc5e356d4a1b3a",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39865673746"
    }
  ]
}