{
  "_id": "6a103d93acfb0bcc41c9c4ed",
  "Package": "Signac",
  "Title": "Analysis of Single-Cell Chromatin Data",
  "Version": "1.17.1",
  "Date": "2026-04-06",
  "Authors@R": "c(\nperson(given = 'Tim', family = 'Stuart', email = 'stuartt@a-star.edu.sg', role = c('aut', 'cre'), comment = c(ORCID = '0000-0002-3044-0897')),\nperson(given = 'Avi', family = 'Srivastava', email = 'asrivastava@wistar.org', role = 'aut', comment = c(ORCID = '0000-0001-9798-2079')),\nperson(given = 'Paul', family = 'Hoffman', email = 'phoffman@nygenome.org', role = 'ctb', comment = c(ORCID = '0000-0002-7693-8957')),\nperson(given = 'Rahul', family = 'Satija', email = 'rsatija@nygenome.org', role = 'ctb', comment = c(ORCID = '0000-0001-9448-8833'))\n)",
  "Description": "A framework for the analysis and exploration of\nsingle-cell chromatin data. The 'Signac' package contains\nfunctions for quantifying single-cell chromatin data, computing\nper-cell quality control metrics, dimension reduction and\nnormalization, visualization, and DNA sequence motif analysis.\nReference: Stuart et al. (2021)\n<doi:10.1038/s41592-021-01282-5>.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "RoxygenNote": "7.3.3",
  "URL": "https://github.com/stuart-lab/signac, https://stuartlab.org/signac",
  "BugReports": "https://github.com/stuart-lab/signac/issues",
  "Collate": "'RcppExports.R' 'Signac-package.R' 'data.R'\n'differential_accessibility.R' 'generics.R'\n'dimension_reduction.R' 'footprinting.R' 'fragments.R'\n'genomeinfodb-methods.R' 'granges-methods.R' 'heatmaps.R'\n'iranges-methods.R' 'links.R' 'mito.R' 'motifs.R' 'objects.R'\n'ontology.R' 'peaks.R' 'preprocessing.R' 'quantification.R'\n'region-enrichment.R' 'utilities.R' 'visualization.R' 'zzz.R'",
  "Roxygen": "list(markdown = TRUE)",
  "Config/pak/sysreqs": "libbz2-dev libicu-dev liblzma-dev libssl-dev\nxz-utils zlib1g-dev",
  "Repository": "https://stuart-lab.r-universe.dev",
  "Date/Publication": "2026-04-06 08:44:46 UTC",
  "RemoteUrl": "https://github.com/stuart-lab/signac",
  "RemoteRef": "HEAD",
  "RemoteSha": "12d1ff82774890b08e55b3101f36fab83e674b88",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-05-11 09:40:47 UTC",
    "User": "root"
  },
  "Author": "Tim Stuart [aut, cre] (ORCID: <https://orcid.org/0000-0002-3044-0897>),\nAvi Srivastava [aut] (ORCID: <https://orcid.org/0000-0001-9798-2079>),\nPaul Hoffman [ctb] (ORCID: <https://orcid.org/0000-0002-7693-8957>),\nRahul Satija [ctb] (ORCID: <https://orcid.org/0000-0001-9448-8833>)",
  "Maintainer": "Tim Stuart <stuartt@a-star.edu.sg>",
  "MD5sum": "97e677327dee79afe0bd381b557f5c28",
  "_user": "stuart-lab",
  "_type": "src",
  "_file": "Signac_1.17.1.tar.gz",
  "_fileid": "44d063102076025ee13d58dc324d2fc8e15e2b9ebc7ba6577a37f4b02482ce59",
  "_filesize": 4352855,
  "_sha256": "44d063102076025ee13d58dc324d2fc8e15e2b9ebc7ba6577a37f4b02482ce59",
  "_created": "2026-05-11T09:40:47.000Z",
  "_published": "2026-05-22T11:27:15.152Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 77370079628,
      "time": 337,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "6915285583"
    },
    {
      "job": 77370078960,
      "time": 391,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "6915304198"
    },
    {
      "job": 77370079402,
      "time": 340,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6915286107"
    },
    {
      "job": 77370079152,
      "time": 372,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6915299858"
    },
    {
      "job": 77370079097,
      "time": 256,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "6915246397"
    },
    {
      "job": 77370079193,
      "time": 621,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "6915372219"
    },
    {
      "job": 77370079037,
      "time": 251,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6915250497"
    },
    {
      "job": 77370078883,
      "time": 588,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6915364124"
    },
    {
      "job": 77370078840,
      "time": 409,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6915172613"
    },
    {
      "job": 77370078655,
      "time": 216,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7159377089"
    },
    {
      "job": 77370079360,
      "time": 340,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "6915285803"
    },
    {
      "job": 77370079393,
      "time": 327,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "6915282234"
    },
    {
      "job": 77370079368,
      "time": 332,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6915283220"
    }
  ],
  "_buildurl": "https://github.com/r-universe/stuart-lab/actions/runs/25662218372",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/stuart-lab/signac",
  "_commit": {
    "id": "12d1ff82774890b08e55b3101f36fab83e674b88",
    "author": "timoast <4591688+timoast@users.noreply.github.com>",
    "committer": "timoast <4591688+timoast@users.noreply.github.com>",
    "message": "remove cache\n",
    "time": 1775465086
  },
  "_maintainer": {
    "name": "Tim Stuart",
    "email": "stuartt@a-star.edu.sg",
    "login": "timoast",
    "orcid": "0000-0002-3044-0897",
    "twitter": "@timoast",
    "uuid": 4591688
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.1.0",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "GenomeInfoDb",
      "version": ">= 1.29.3",
      "role": "Imports"
    },
    {
      "package": "GenomicRanges",
      "role": "Imports"
    },
    {
      "package": "IRanges",
      "role": "Imports"
    },
    {
      "package": "Matrix",
      "role": "Imports"
    },
    {
      "package": "Rsamtools",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "SeuratObject",
      "version": ">= 5.0.2",
      "role": "Imports"
    },
    {
      "package": "data.table",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "version": ">= 1.0.0",
      "role": "Imports"
    },
    {
      "package": "future",
      "role": "Imports"
    },
    {
      "package": "future.apply",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "pbapply",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "patchwork",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "BiocGenerics",
      "role": "Imports"
    },
    {
      "package": "stringi",
      "role": "Imports"
    },
    {
      "package": "fastmatch",
      "role": "Imports"
    },
    {
      "package": "RcppRoll",
      "role": "Imports"
    },
    {
      "package": "scales",
      "role": "Imports"
    },
    {
      "package": "Rcpp",
      "role": "Imports"
    },
    {
      "package": "grid",
      "role": "Imports"
    },
    {
      "package": "tidyselect",
      "role": "Imports"
    },
    {
      "package": "vctrs",
      "role": "Imports"
    },
    {
      "package": "lifecycle",
      "role": "Imports"
    },
    {
      "package": "sparseMatrixStats",
      "role": "Imports"
    },
    {
      "package": "RSpectra",
      "role": "Imports"
    },
    {
      "package": "Seurat",
      "version": ">= 5.0.2",
      "role": "Suggests"
    },
    {
      "package": "ggforce",
      "role": "Suggests"
    },
    {
      "package": "ggrepel",
      "role": "Suggests"
    },
    {
      "package": "ggseqlogo",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 2.1.0",
      "role": "Suggests"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Suggests"
    },
    {
      "package": "TFBSTools",
      "role": "Suggests"
    },
    {
      "package": "motifmatchr",
      "role": "Suggests"
    },
    {
      "package": "BSgenome",
      "role": "Suggests"
    },
    {
      "package": "shiny",
      "role": "Suggests"
    },
    {
      "package": "miniUI",
      "role": "Suggests"
    },
    {
      "package": "rtracklayer",
      "role": "Suggests"
    },
    {
      "package": "biovizBase",
      "role": "Suggests"
    },
    {
      "package": "Biostrings",
      "role": "Suggests"
    },
    {
      "package": "lsa",
      "role": "Suggests"
    },
    {
      "package": "MASS",
      "role": "Suggests"
    },
    {
      "package": "wrswoR",
      "role": "Suggests"
    },
    {
      "package": "fgsea",
      "role": "Suggests"
    }
  ],
  "_owner": "stuart-lab",
  "_selfowned": true,
  "_usedby": 3,
  "_updates": [
    {
      "week": "2025-29",
      "n": 6
    },
    {
      "week": "2025-31",
      "n": 1
    },
    {
      "week": "2025-34",
      "n": 7
    },
    {
      "week": "2025-36",
      "n": 5
    },
    {
      "week": "2025-41",
      "n": 4
    },
    {
      "week": "2025-45",
      "n": 12
    },
    {
      "week": "2025-46",
      "n": 7
    },
    {
      "week": "2025-48",
      "n": 3
    },
    {
      "week": "2025-49",
      "n": 8
    },
    {
      "week": "2025-50",
      "n": 4
    },
    {
      "week": "2026-04",
      "n": 1
    },
    {
      "week": "2026-14",
      "n": 22
    },
    {
      "week": "2026-15",
      "n": 5
    }
  ],
  "_tags": [
    {
      "name": "1.15.0",
      "date": "2025-08-19"
    },
    {
      "name": "1.16.0",
      "date": "2025-10-10"
    },
    {
      "name": "1.17.0",
      "date": "2026-04-02"
    },
    {
      "name": "1.17.1",
      "date": "2026-04-06"
    }
  ],
  "_topics": [
    "atac",
    "bioinformatics",
    "single-cell",
    "zlib",
    "cpp"
  ],
  "_stars": 415,
  "_contributors": [
    {
      "user": "timoast",
      "count": 2141,
      "uuid": 4591688
    },
    {
      "user": "saketkc",
      "count": 14,
      "uuid": 682153
    },
    {
      "user": "javentyr",
      "count": 12,
      "uuid": 84190597
    },
    {
      "user": "k3yavi",
      "count": 11,
      "uuid": 8772521
    },
    {
      "user": "puriney",
      "count": 5,
      "uuid": 1233372
    },
    {
      "user": "gesmira",
      "count": 4,
      "uuid": 59940281
    },
    {
      "user": "kmwinkley",
      "count": 4,
      "uuid": 23247951
    },
    {
      "user": "iandriver",
      "count": 2,
      "uuid": 2230336
    },
    {
      "user": "hoondy",
      "count": 1,
      "uuid": 6531609
    },
    {
      "user": "federicomarini",
      "count": 1,
      "uuid": 7447478
    },
    {
      "user": "jeroen",
      "count": 1,
      "uuid": 216319
    },
    {
      "user": "lldelisle",
      "count": 1,
      "uuid": 30404086
    },
    {
      "user": "nrockweiler",
      "count": 1,
      "uuid": 8428293
    },
    {
      "user": "chenyenchung",
      "count": 1,
      "uuid": 22821107
    },
    {
      "user": "cmfffff",
      "count": 1,
      "uuid": 59285691
    },
    {
      "user": "maxim-h",
      "count": 1,
      "uuid": 22867431
    }
  ],
  "_userbio": {
    "uuid": 102445397,
    "type": "organization",
    "name": "Stuart Lab"
  },
  "_downloads": {
    "count": 10816,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/Signac"
  },
  "_mentions": 24,
  "_devurl": "https://github.com/stuart-lab/signac",
  "_pkgdown": "https://stuartlab.org/signac",
  "_searchresults": 7104,
  "_rbuild": "4.6.0",
  "_assets": [
    "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",
    "extra/Signac.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/stuart-lab/signac",
  "_realowner": "stuart-lab",
  "_cranurl": true,
  "_releases": [
    {
      "version": "0.2.4",
      "date": "2020-03-13"
    },
    {
      "version": "0.2.5",
      "date": "2020-04-16"
    },
    {
      "version": "1.0.0",
      "date": "2020-08-16"
    },
    {
      "version": "1.1.0",
      "date": "2020-11-07"
    },
    {
      "version": "1.1.1",
      "date": "2021-02-04"
    },
    {
      "version": "1.2.0",
      "date": "2021-04-28"
    },
    {
      "version": "1.2.1",
      "date": "2021-05-11"
    },
    {
      "version": "1.3.0",
      "date": "2021-07-12"
    },
    {
      "version": "1.4.0",
      "date": "2021-09-22"
    },
    {
      "version": "1.5.0",
      "date": "2021-12-08"
    },
    {
      "version": "1.6.0",
      "date": "2022-03-05"
    },
    {
      "version": "1.7.0",
      "date": "2022-06-01"
    },
    {
      "version": "1.8.0",
      "date": "2022-09-21"
    },
    {
      "version": "1.9.0",
      "date": "2022-12-08"
    },
    {
      "version": "1.10.0",
      "date": "2023-05-30"
    },
    {
      "version": "1.11.0",
      "date": "2023-10-13"
    },
    {
      "version": "1.12.0",
      "date": "2023-11-08"
    },
    {
      "version": "1.13.0",
      "date": "2024-04-04"
    },
    {
      "version": "1.14.0",
      "date": "2024-08-21"
    },
    {
      "version": "1.15.0",
      "date": "2025-08-18"
    },
    {
      "version": "1.16.0",
      "date": "2025-10-10"
    },
    {
      "version": "1.17.0",
      "date": "2026-04-01"
    },
    {
      "version": "1.17.1",
      "date": "2026-04-06"
    }
  ],
  "_exports": [
    "AccessiblePeaks",
    "AddMotifs",
    "AggregateTiles",
    "AlleleFreq",
    "Annotation",
    "Annotation<-",
    "AnnotationPlot",
    "as.ChromatinAssay",
    "ATACqc",
    "AverageCounts",
    "BigwigTrack",
    "BinarizeCounts",
    "CallPeaks",
    "Cells",
    "Cells<-",
    "CellsPerGroup",
    "ClosestFeature",
    "ClusterClonotypes",
    "CombineTracks",
    "ConnectionsToLinks",
    "ConvertMotifID",
    "corSparse",
    "CountFragments",
    "CountsInRegion",
    "coverage",
    "CoverageBrowser",
    "CoveragePlot",
    "CreateChromatinAssay",
    "CreateFragmentObject",
    "CreateMotifMatrix",
    "CreateMotifObject",
    "DensityScatter",
    "DepthCor",
    "disjoin",
    "disjointBins",
    "distance",
    "distanceToNearest",
    "DownsampleFeatures",
    "EnrichedTerms",
    "ExpressionPlot",
    "Extend",
    "FeatureMatrix",
    "FilterCells",
    "FindClonotypes",
    "FindMotifs",
    "findOverlaps",
    "FindTopFeatures",
    "FitMeanVar",
    "follow",
    "Footprint",
    "FractionCountsInRegion",
    "FragmentHistogram",
    "Fragments",
    "Fragments<-",
    "FRiP",
    "gaps",
    "GeneActivity",
    "genome",
    "genome<-",
    "GenomeBinMatrix",
    "GetCellsInRegion",
    "GetFootprintData",
    "GetFragmentData",
    "GetGRangesFromEnsDb",
    "GetIntersectingFeatures",
    "GetLinkedGenes",
    "GetLinkedPeaks",
    "GetMotifData",
    "GetTSSPositions",
    "granges",
    "GRangesToString",
    "IdentifyVariants",
    "InsertionBias",
    "IntersectMatrix",
    "isCircular",
    "isCircular<-",
    "isDisjoint",
    "Jaccard",
    "LinkPeaks",
    "LinkPlot",
    "Links",
    "Links<-",
    "LookupGeneCoords",
    "MatchRegionStats",
    "MotifCounts",
    "MotifPlot",
    "Motifs",
    "Motifs<-",
    "nearest",
    "NucleosomeSignal",
    "PeakPlot",
    "PearsonResidualVar",
    "PlotFootprint",
    "precede",
    "ReadMGATK",
    "reduce",
    "RegionHeatmap",
    "RegionMatrix",
    "RegionPlot",
    "RegionStats",
    "RunSVD",
    "RunTFIDF",
    "seqinfo",
    "seqinfo<-",
    "seqlengths",
    "seqlengths<-",
    "seqlevels",
    "seqlevels<-",
    "seqnames",
    "seqnames<-",
    "SetMotifData",
    "SortIdents",
    "SplitFragments",
    "StringToGRanges",
    "SubsetMatrix",
    "theme_browser",
    "TilePlot",
    "TSSEnrichment",
    "TSSPlot",
    "UnifyPeaks",
    "UpdatePath",
    "ValidateCells",
    "ValidateFragments",
    "ValidateHash",
    "VariantPlot"
  ],
  "_datasets": [
    {
      "name": "atac_small",
      "title": "A small example scATAC-seq dataset",
      "object": "atac_small",
      "class": [
        "Seurat"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "blacklist_ce10",
      "title": "Genomic blacklist regions for C. elegans ce10 (0-based)",
      "object": "blacklist_ce10",
      "class": [
        "DeprecatedGRanges"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "blacklist_ce11",
      "title": "Genomic blacklist regions for C. elegans ce11 (0-based)",
      "object": "blacklist_ce11",
      "class": [
        "DeprecatedGRanges"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "blacklist_dm3",
      "title": "Genomic blacklist regions for Drosophila dm3 (0-based)",
      "object": "blacklist_dm3",
      "class": [
        "DeprecatedGRanges"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "blacklist_dm6",
      "title": "Genomic blacklist regions for Drosophila dm6 (0-based)",
      "object": "blacklist_dm6",
      "class": [
        "DeprecatedGRanges"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "blacklist_hg19",
      "title": "Genomic blacklist regions for Human hg19 (0-based)",
      "object": "blacklist_hg19",
      "class": [
        "DeprecatedGRanges"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "blacklist_hg38",
      "title": "Genomic blacklist regions for Human GRCh38",
      "object": "blacklist_hg38",
      "class": [
        "DeprecatedGRanges"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "blacklist_hg38_unified",
      "title": "Unified genomic blacklist regions for Human GRCh38",
      "object": "blacklist_hg38_unified",
      "class": [
        "DeprecatedGRanges"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "blacklist_mm10",
      "title": "Genomic blacklist regions for Mouse mm10 (0-based)",
      "object": "blacklist_mm10",
      "class": [
        "DeprecatedGRanges"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "AccessiblePeaks",
      "title": "Accessible peaks",
      "concept": [
        "utilities"
      ],
      "topics": [
        "AccessiblePeaks"
      ]
    },
    {
      "page": "AddMotifs",
      "title": "Add DNA sequence motif information",
      "concept": [
        "motifs"
      ],
      "topics": [
        "AddMotifs",
        "AddMotifs.Assay",
        "AddMotifs.ChromatinAssay",
        "AddMotifs.default",
        "AddMotifs.Seurat",
        "AddMotifs.StdAssay"
      ]
    },
    {
      "page": "AggregateTiles",
      "title": "Quantify aggregated genome tiles",
      "concept": [
        "quantification"
      ],
      "topics": [
        "AggregateTiles",
        "AggregateTiles.ChromatinAssay",
        "AggregateTiles.default",
        "AggregateTiles.Seurat"
      ]
    },
    {
      "page": "AlleleFreq",
      "title": "Compute allele frequencies per cell",
      "concept": [
        "mito"
      ],
      "topics": [
        "AlleleFreq",
        "AlleleFreq.Assay",
        "AlleleFreq.default",
        "AlleleFreq.Seurat",
        "AlleleFreq.StdAssay"
      ]
    },
    {
      "page": "Annotation",
      "title": "Annotation",
      "concept": [
        "assay"
      ],
      "topics": [
        "Annotation",
        "Annotation.ChromatinAssay",
        "Annotation.Seurat",
        "Annotation<-",
        "Annotation<-.ChromatinAssay",
        "Annotation<-.Seurat"
      ]
    },
    {
      "page": "AnnotationPlot",
      "title": "Plot gene annotations",
      "concept": [
        "visualization"
      ],
      "topics": [
        "AnnotationPlot"
      ]
    },
    {
      "page": "as.ChromatinAssay",
      "title": "Convert objects to a ChromatinAssay",
      "concept": [
        "assay"
      ],
      "topics": [
        "as.ChromatinAssay",
        "as.ChromatinAssay.Assay"
      ]
    },
    {
      "page": "atac_small",
      "title": "A small example scATAC-seq dataset",
      "concept": [
        "data"
      ],
      "topics": [
        "atac_small"
      ]
    },
    {
      "page": "ATACqc",
      "title": "Compute scATAC-seq QC metrics",
      "concept": [
        "qc"
      ],
      "topics": [
        "ATACqc",
        "ATACqc.ChromatinAssay",
        "ATACqc.default",
        "ATACqc.Seurat"
      ]
    },
    {
      "page": "AverageCounts",
      "title": "Average Counts",
      "concept": [
        "utilities"
      ],
      "topics": [
        "AverageCounts"
      ]
    },
    {
      "page": "BigwigTrack",
      "title": "Plot data from BigWig files",
      "concept": [
        "visualization"
      ],
      "topics": [
        "BigwigTrack"
      ]
    },
    {
      "page": "BinarizeCounts",
      "title": "Binarize counts",
      "concept": [
        "preprocessing"
      ],
      "topics": [
        "BinarizeCounts",
        "BinarizeCounts.Assay",
        "BinarizeCounts.default",
        "BinarizeCounts.Seurat"
      ]
    },
    {
      "page": "blacklist_ce10",
      "title": "Genomic blacklist regions for C. elegans ce10 (0-based)",
      "concept": [
        "data"
      ],
      "topics": [
        "blacklist_ce10"
      ]
    },
    {
      "page": "blacklist_ce11",
      "title": "Genomic blacklist regions for C. elegans ce11 (0-based)",
      "concept": [
        "data"
      ],
      "topics": [
        "blacklist_ce11"
      ]
    },
    {
      "page": "blacklist_dm3",
      "title": "Genomic blacklist regions for Drosophila dm3 (0-based)",
      "concept": [
        "data"
      ],
      "topics": [
        "blacklist_dm3"
      ]
    },
    {
      "page": "blacklist_dm6",
      "title": "Genomic blacklist regions for Drosophila dm6 (0-based)",
      "concept": [
        "data"
      ],
      "topics": [
        "blacklist_dm6"
      ]
    },
    {
      "page": "blacklist_hg19",
      "title": "Genomic blacklist regions for Human hg19 (0-based)",
      "concept": [
        "data"
      ],
      "topics": [
        "blacklist_hg19"
      ]
    },
    {
      "page": "blacklist_hg38",
      "title": "Genomic blacklist regions for Human GRCh38",
      "concept": [
        "data"
      ],
      "topics": [
        "blacklist_hg38"
      ]
    },
    {
      "page": "blacklist_hg38_unified",
      "title": "Unified genomic blacklist regions for Human GRCh38",
      "concept": [
        "data"
      ],
      "topics": [
        "blacklist_hg38_unified"
      ]
    },
    {
      "page": "blacklist_mm10",
      "title": "Genomic blacklist regions for Mouse mm10 (0-based)",
      "concept": [
        "data"
      ],
      "topics": [
        "blacklist_mm10"
      ]
    },
    {
      "page": "CallPeaks",
      "title": "Call peaks",
      "concept": [
        "quantification"
      ],
      "topics": [
        "CallPeaks",
        "CallPeaks.ChromatinAssay",
        "CallPeaks.default",
        "CallPeaks.Fragment",
        "CallPeaks.Seurat"
      ]
    },
    {
      "page": "Cells",
      "title": "Set and get cell barcode information for a 'Fragment()' object",
      "concept": [
        "fragments"
      ],
      "topics": [
        "Cells.Fragment",
        "Cells<-.Fragment"
      ]
    },
    {
      "page": "Cells-set",
      "title": "Set and get cell barcode information for a Fragment object",
      "concept": [
        "assay"
      ],
      "topics": [
        "Cells<-"
      ]
    },
    {
      "page": "CellsPerGroup",
      "title": "Cells per group",
      "concept": [
        "utilities"
      ],
      "topics": [
        "CellsPerGroup"
      ]
    },
    {
      "page": "ChromatinAssay-class",
      "title": "The ChromatinAssay class",
      "concept": [
        "assay"
      ],
      "topics": [
        "ChromatinAssay",
        "ChromatinAssay-class"
      ]
    },
    {
      "page": "ClosestFeature",
      "title": "Closest Feature",
      "concept": [
        "utilities"
      ],
      "topics": [
        "ClosestFeature"
      ]
    },
    {
      "page": "ClusterClonotypes",
      "title": "Find relationships between clonotypes",
      "concept": [
        "mito"
      ],
      "topics": [
        "ClusterClonotypes"
      ]
    },
    {
      "page": "CombineTracks",
      "title": "Combine genome region plots",
      "concept": [
        "visualization"
      ],
      "topics": [
        "CombineTracks"
      ]
    },
    {
      "page": "ConnectionsToLinks",
      "title": "Cicero connections to links",
      "concept": [
        "links"
      ],
      "topics": [
        "ConnectionsToLinks"
      ]
    },
    {
      "page": "ConvertMotifID",
      "title": "Convert between motif name and motif ID",
      "concept": [
        "motifs"
      ],
      "topics": [
        "ConvertMotifID",
        "ConvertMotifID.Assay",
        "ConvertMotifID.ChromatinAssay",
        "ConvertMotifID.default",
        "ConvertMotifID.Motif",
        "ConvertMotifID.Seurat",
        "ConvertMotifID.StdAssay"
      ]
    },
    {
      "page": "CountFragments",
      "title": "Count fragments",
      "concept": [
        "fragments"
      ],
      "topics": [
        "CountFragments"
      ]
    },
    {
      "page": "CountsInRegion",
      "title": "Counts in region",
      "concept": [
        "utilities"
      ],
      "topics": [
        "CountsInRegion"
      ]
    },
    {
      "page": "coverage-ChromatinAssay-method",
      "title": "Coverage of a ChromatinAssay object",
      "concept": [
        "coverage"
      ],
      "topics": [
        "coverage",
        "coverage,ChromatinAssay-method",
        "coverage,Seurat-method"
      ]
    },
    {
      "page": "CoverageBrowser",
      "title": "Genome browser",
      "concept": [
        "visualization"
      ],
      "topics": [
        "CoverageBrowser"
      ]
    },
    {
      "page": "CoveragePlot",
      "title": "Plot Tn5 insertion frequency over a region",
      "concept": [
        "visualization"
      ],
      "topics": [
        "CoveragePlot"
      ]
    },
    {
      "page": "CreateChromatinAssay",
      "title": "Create ChromatinAssay object",
      "concept": [
        "assay"
      ],
      "topics": [
        "CreateChromatinAssay"
      ]
    },
    {
      "page": "CreateFragmentObject",
      "title": "Create a Fragment object",
      "concept": [
        "fragments"
      ],
      "topics": [
        "CreateFragmentObject"
      ]
    },
    {
      "page": "CreateMotifMatrix",
      "title": "Create motif matrix",
      "concept": [
        "motifs",
        "preprocessing"
      ],
      "topics": [
        "CreateMotifMatrix"
      ]
    },
    {
      "page": "CreateMotifObject",
      "title": "Create motif object",
      "concept": [
        "motifs"
      ],
      "topics": [
        "CreateMotifObject"
      ]
    },
    {
      "page": "DensityScatter",
      "title": "Scatterplot colored by point density",
      "concept": [
        "visualization"
      ],
      "topics": [
        "DensityScatter"
      ]
    },
    {
      "page": "DepthCor",
      "title": "Plot sequencing depth correlation",
      "concept": [
        "visualization"
      ],
      "topics": [
        "DepthCor"
      ]
    },
    {
      "page": "DownsampleFeatures",
      "title": "Downsample Features",
      "concept": [
        "preprocessing"
      ],
      "topics": [
        "DownsampleFeatures"
      ]
    },
    {
      "page": "EnrichedTerms",
      "title": "Find enriched ontology terms",
      "concept": [
        "utilities"
      ],
      "topics": [
        "EnrichedTerms"
      ]
    },
    {
      "page": "ExpressionPlot",
      "title": "Plot gene expression",
      "concept": [
        "visualization"
      ],
      "topics": [
        "ExpressionPlot"
      ]
    },
    {
      "page": "Extend",
      "title": "Extend",
      "concept": [
        "utilities"
      ],
      "topics": [
        "Extend"
      ]
    },
    {
      "page": "FeatureMatrix",
      "title": "Feature Matrix",
      "concept": [
        "quantification"
      ],
      "topics": [
        "FeatureMatrix"
      ]
    },
    {
      "page": "FilterCells",
      "title": "Filter cells from fragment file",
      "concept": [
        "fragments"
      ],
      "topics": [
        "FilterCells"
      ]
    },
    {
      "page": "FindClonotypes",
      "title": "Find clonotypes",
      "concept": [
        "mito"
      ],
      "topics": [
        "FindClonotypes"
      ]
    },
    {
      "page": "FindMotifs",
      "title": "FindMotifs",
      "concept": [
        "motifs"
      ],
      "topics": [
        "FindMotifs"
      ]
    },
    {
      "page": "findOverlaps-methods",
      "title": "Find overlapping ranges for ChromatinAssay objects",
      "concept": [
        "overlaps"
      ],
      "topics": [
        "countOverlaps",
        "countOverlaps,ChromatinAssay,ChromatinAssay-method",
        "countOverlaps,ChromatinAssay,Vector-method",
        "countOverlaps,Seurat,Seurat-method",
        "countOverlaps,Seurat,Vector-method",
        "countOverlaps,Vector,ChromatinAssay-method",
        "countOverlaps,Vector,Seurat-method",
        "findOverlaps",
        "findOverlaps,ChromatinAssay,ChromatinAssay-method",
        "findOverlaps,ChromatinAssay,Vector-method",
        "findOverlaps,Seurat,Seurat-method",
        "findOverlaps,Seurat,Vector-method",
        "findOverlaps,Vector,ChromatinAssay-method",
        "findOverlaps,Vector,Seurat-method",
        "findOverlaps-methods"
      ]
    },
    {
      "page": "FindTopFeatures",
      "title": "Find most frequently observed features",
      "concept": [
        "preprocessing"
      ],
      "topics": [
        "FindTopFeatures",
        "FindTopFeatures.Assay",
        "FindTopFeatures.default",
        "FindTopFeatures.Seurat",
        "FindTopFeatures.StdAssay"
      ]
    },
    {
      "page": "FitMeanVar",
      "title": "Find variable features fitting LOESS",
      "concept": [
        "preprocessing"
      ],
      "topics": [
        "FitMeanVar",
        "FitMeanVar.Assay",
        "FitMeanVar.data.frame",
        "FitMeanVar.default",
        "FitMeanVar.Seurat",
        "FitMeanVar.StdAssay"
      ]
    },
    {
      "page": "Footprint",
      "title": "Transcription factor footprinting analysis",
      "concept": [
        "footprinting"
      ],
      "topics": [
        "Footprint",
        "Footprint.ChromatinAssay",
        "Footprint.Seurat"
      ]
    },
    {
      "page": "FractionCountsInRegion",
      "title": "Fraction of counts in a genomic region",
      "concept": [
        "utilities"
      ],
      "topics": [
        "FractionCountsInRegion"
      ]
    },
    {
      "page": "Fragment-class",
      "title": "The Fragment class",
      "concept": [
        "fragments"
      ],
      "topics": [
        "Fragment",
        "Fragment-class"
      ]
    },
    {
      "page": "FragmentHistogram",
      "title": "Plot fragment length histogram",
      "concept": [
        "qc",
        "visualization"
      ],
      "topics": [
        "FragmentHistogram"
      ]
    },
    {
      "page": "Fragments",
      "title": "Get the Fragment objects",
      "concept": [
        "assay",
        "fragments"
      ],
      "topics": [
        "Fragments",
        "Fragments.ChromatinAssay",
        "Fragments.Seurat",
        "Fragments<-",
        "Fragments<-.ChromatinAssay",
        "Fragments<-.Seurat"
      ]
    },
    {
      "page": "FRiP",
      "title": "Calculate fraction of reads in peaks per cell",
      "concept": [
        "qc"
      ],
      "topics": [
        "FRiP"
      ]
    },
    {
      "page": "GeneActivity",
      "title": "Create gene activity matrix",
      "concept": [
        "utilities"
      ],
      "topics": [
        "GeneActivity"
      ]
    },
    {
      "page": "GenomeBinMatrix",
      "title": "Genome bin matrix",
      "concept": [
        "quantification"
      ],
      "topics": [
        "GenomeBinMatrix"
      ]
    },
    {
      "page": "GetCellsInRegion",
      "title": "Get cells in a region",
      "concept": [
        "utilities"
      ],
      "topics": [
        "GetCellsInRegion"
      ]
    },
    {
      "page": "GetFootprintData",
      "title": "Get footprinting data",
      "concept": [
        "footprinting"
      ],
      "topics": [
        "GetFootprintData"
      ]
    },
    {
      "page": "GetFragmentData",
      "title": "Get Fragment object data",
      "concept": [
        "assay"
      ],
      "topics": [
        "GetFragmentData"
      ]
    },
    {
      "page": "GetGRangesFromEnsDb",
      "title": "Extract genomic ranges from EnsDb object",
      "concept": [
        "utilities"
      ],
      "topics": [
        "GetGRangesFromEnsDb"
      ]
    },
    {
      "page": "GetIntersectingFeatures",
      "title": "Find intersecting regions between two objects",
      "concept": [
        "utilities"
      ],
      "topics": [
        "GetIntersectingFeatures"
      ]
    },
    {
      "page": "GetLinkedGenes",
      "title": "Get genes linked to peaks",
      "concept": [
        "links"
      ],
      "topics": [
        "GetLinkedGenes"
      ]
    },
    {
      "page": "GetLinkedPeaks",
      "title": "Get peaks linked to genes",
      "concept": [
        "links"
      ],
      "topics": [
        "GetLinkedPeaks"
      ]
    },
    {
      "page": "GetMotifData",
      "title": "Retrieve a motif matrix",
      "concept": [
        "motifs"
      ],
      "topics": [
        "GetMotifData",
        "GetMotifData.ChromatinAssay",
        "GetMotifData.Motif",
        "GetMotifData.Seurat"
      ]
    },
    {
      "page": "GetTSSPositions",
      "title": "Find transcriptional start sites",
      "concept": [
        "utilities"
      ],
      "topics": [
        "GetTSSPositions"
      ]
    },
    {
      "page": "granges-methods",
      "title": "Access genomic ranges for ChromatinAssay objects",
      "concept": [
        "granges"
      ],
      "topics": [
        "granges",
        "granges,ChromatinAssay-method",
        "granges,Seurat-method",
        "granges-methods"
      ]
    },
    {
      "page": "GRangesToString",
      "title": "GRanges to String",
      "concept": [
        "utilities"
      ],
      "topics": [
        "GRangesToString"
      ]
    },
    {
      "page": "head.Fragment",
      "title": "Return the first rows of a fragment file",
      "concept": [
        "fragments"
      ],
      "topics": [
        "head.Fragment"
      ]
    },
    {
      "page": "IdentifyVariants",
      "title": "Identify mitochondrial variants",
      "concept": [
        "mito"
      ],
      "topics": [
        "IdentifyVariants",
        "IdentifyVariants.Assay",
        "IdentifyVariants.default",
        "IdentifyVariants.Seurat",
        "IdentifyVariants.StdAssay"
      ]
    },
    {
      "page": "InsertionBias",
      "title": "Compute Tn5 insertion bias",
      "concept": [
        "footprinting"
      ],
      "topics": [
        "InsertionBias",
        "InsertionBias.ChromatinAssay",
        "InsertionBias.Seurat"
      ]
    },
    {
      "page": "inter-range-methods",
      "title": "Inter-range transformations for ChromatinAssay objects",
      "concept": [
        "inter_range"
      ],
      "topics": [
        "disjoin",
        "disjoin,ChromatinAssay-method",
        "disjoin,Seurat-method",
        "disjointBins",
        "disjointBins,ChromatinAssay-method",
        "disjointBins,Seurat-method",
        "gaps",
        "gaps,ChromatinAssay-method",
        "gaps,Seurat-method",
        "inter-range-methods",
        "isDisjoint",
        "isDisjoint,ChromatinAssay-method",
        "isDisjoint,Seurat-method",
        "range",
        "range,ChromatinAssay-method",
        "range,Seurat-method",
        "reduce",
        "reduce,ChromatinAssay-method",
        "reduce,Seurat-method"
      ]
    },
    {
      "page": "IntersectMatrix",
      "title": "Intersect genomic coordinates with matrix rows",
      "concept": [
        "utilities"
      ],
      "topics": [
        "IntersectMatrix"
      ]
    },
    {
      "page": "Jaccard",
      "title": "Calculate the Jaccard index between two matrices",
      "concept": [
        "dimension_reduction"
      ],
      "topics": [
        "Jaccard"
      ]
    },
    {
      "page": "LinkPeaks",
      "title": "Link peaks to genes",
      "concept": [
        "links"
      ],
      "topics": [
        "LinkPeaks"
      ]
    },
    {
      "page": "LinkPlot",
      "title": "Plot linked genomic elements",
      "concept": [
        "links",
        "visualization"
      ],
      "topics": [
        "LinkPlot"
      ]
    },
    {
      "page": "Links",
      "title": "Get or set links information",
      "concept": [
        "assay",
        "links"
      ],
      "topics": [
        "Links",
        "Links.ChromatinAssay",
        "Links.Seurat",
        "Links<-",
        "Links<-.ChromatinAssay",
        "Links<-.Seurat"
      ]
    },
    {
      "page": "LookupGeneCoords",
      "title": "Get gene coordinates",
      "concept": [
        "utilities"
      ],
      "topics": [
        "LookupGeneCoords"
      ]
    },
    {
      "page": "MatchRegionStats",
      "title": "Match DNA sequence characteristics",
      "concept": [
        "motifs",
        "utilities"
      ],
      "topics": [
        "MatchRegionStats"
      ]
    },
    {
      "page": "Motif-class",
      "title": "The Motif class",
      "concept": [
        "motifs"
      ],
      "topics": [
        "Motif",
        "Motif-class"
      ]
    },
    {
      "page": "MotifCounts",
      "title": "Count fragments surrounding motif sites",
      "concept": [
        "motifs"
      ],
      "topics": [
        "MotifCounts"
      ]
    },
    {
      "page": "MotifPlot",
      "title": "Plot DNA sequence motif",
      "concept": [
        "motifs",
        "visualization"
      ],
      "topics": [
        "MotifPlot"
      ]
    },
    {
      "page": "Motifs",
      "title": "Get or set a motif information",
      "concept": [
        "assay",
        "motifs"
      ],
      "topics": [
        "Motifs",
        "Motifs.ChromatinAssay",
        "Motifs.Seurat",
        "Motifs<-",
        "Motifs<-.ChromatinAssay",
        "Motifs<-.Seurat"
      ]
    },
    {
      "page": "nearest-methods",
      "title": "Find the nearest range neighbors for ChromatinAssay objects",
      "concept": [
        "nearest"
      ],
      "topics": [
        "distance",
        "distance,ANY,ChromatinAssay-method",
        "distance,ANY,Seurat-method",
        "distance,ChromatinAssay,ANY-method",
        "distance,ChromatinAssay,ChromatinAssay-method",
        "distance,Seurat,ANY-method",
        "distance,Seurat,Seurat-method",
        "distanceToNearest",
        "distanceToNearest,ANY,ChromatinAssay-method",
        "distanceToNearest,ANY,Seurat-method",
        "distanceToNearest,ChromatinAssay,ANY-method",
        "distanceToNearest,ChromatinAssay,ChromatinAssay-method",
        "distanceToNearest,Seurat,ANY-method",
        "distanceToNearest,Seurat,Seurat-method",
        "follow",
        "follow,ANY,ChromatinAssay-method",
        "follow,ANY,Seurat-method",
        "follow,ChromatinAssay,ANY-method",
        "follow,ChromatinAssay,ChromatinAssay-method",
        "follow,Seurat,ANY-method",
        "follow,Seurat,Seurat-method",
        "nearest",
        "nearest,ANY,ChromatinAssay-method",
        "nearest,ANY,Seurat-method",
        "nearest,ChromatinAssay,ANY-method",
        "nearest,ChromatinAssay,ChromatinAssay-method",
        "nearest,Seurat,ANY-method",
        "nearest,Seurat,Seurat-method",
        "nearest-methods",
        "precede",
        "precede,ANY,ChromatinAssay-method",
        "precede,ANY,Seurat-method",
        "precede,ChromatinAssay,ANY-method",
        "precede,ChromatinAssay,ChromatinAssay-method",
        "precede,Seurat,ANY-method",
        "precede,Seurat,Seurat-method"
      ]
    },
    {
      "page": "NucleosomeSignal",
      "title": "NucleosomeSignal",
      "concept": [
        "qc"
      ],
      "topics": [
        "NucleosomeSignal"
      ]
    },
    {
      "page": "PeakPlot",
      "title": "Plot peaks in a genomic region",
      "concept": [
        "visualization"
      ],
      "topics": [
        "PeakPlot"
      ]
    },
    {
      "page": "PearsonResidualVar",
      "title": "Compute analytic Pearson residual variance",
      "concept": [
        "preprocessing"
      ],
      "topics": [
        "PearsonResidualVar",
        "PearsonResidualVar.Assay",
        "PearsonResidualVar.default",
        "PearsonResidualVar.Seurat",
        "PearsonResidualVar.StdAssay"
      ]
    },
    {
      "page": "PlotFootprint",
      "title": "Plot motif footprinting results",
      "concept": [
        "footprinting",
        "visualization"
      ],
      "topics": [
        "PlotFootprint"
      ]
    },
    {
      "page": "ReadMGATK",
      "title": "Read MGATK output",
      "concept": [
        "mito"
      ],
      "topics": [
        "ReadMGATK"
      ]
    },
    {
      "page": "RegionHeatmap",
      "title": "Region heatmap",
      "concept": [
        "heatmap",
        "visualization"
      ],
      "topics": [
        "RegionHeatmap"
      ]
    },
    {
      "page": "RegionMatrix",
      "title": "Region enrichment analysis",
      "concept": [
        "heatmap"
      ],
      "topics": [
        "RegionMatrix",
        "RegionMatrix.ChromatinAssay",
        "RegionMatrix.default",
        "RegionMatrix.Seurat"
      ]
    },
    {
      "page": "RegionPlot",
      "title": "Region plot",
      "concept": [
        "heatmap",
        "visualization"
      ],
      "topics": [
        "RegionPlot"
      ]
    },
    {
      "page": "RegionStats",
      "title": "Compute base composition information for genomic ranges",
      "concept": [
        "motifs"
      ],
      "topics": [
        "RegionStats",
        "RegionStats.ChromatinAssay",
        "RegionStats.default",
        "RegionStats.Seurat"
      ]
    },
    {
      "page": "RunSVD",
      "title": "Run singular value decomposition",
      "concept": [
        "dimension_reduction"
      ],
      "topics": [
        "RunSVD",
        "RunSVD.Assay",
        "RunSVD.default",
        "RunSVD.Seurat",
        "RunSVD.StdAssay"
      ]
    },
    {
      "page": "RunTFIDF",
      "title": "Compute the term-frequency inverse-document-frequency",
      "concept": [
        "preprocessing"
      ],
      "topics": [
        "RunTFIDF",
        "RunTFIDF.Assay",
        "RunTFIDF.default",
        "RunTFIDF.Seurat",
        "RunTFIDF.StdAssay"
      ]
    },
    {
      "page": "seqinfo-methods",
      "title": "Access and modify sequence information for ChromatinAssay objects",
      "concept": [
        "seqinfo"
      ],
      "topics": [
        "genome",
        "genome,ChromatinAssay-method",
        "genome,Seurat-method",
        "genome<-,ChromatinAssay-method",
        "genome<-,Seurat-method",
        "isCircular",
        "isCircular,ChromatinAssay-method",
        "isCircular,Seurat-method",
        "isCircular<-,ChromatinAssay-method",
        "isCircular<-,Seurat-method",
        "seqinfo",
        "seqinfo,ChromatinAssay-method",
        "seqinfo,Seurat-method",
        "seqinfo-methods",
        "seqinfo<-,ChromatinAssay-method",
        "seqinfo<-,Seurat-method",
        "seqlengths",
        "seqlengths,ChromatinAssay-method",
        "seqlengths,Seurat-method",
        "seqlengths<-,ChromatinAssay-method",
        "seqlengths<-,Seurat-method",
        "seqlevels",
        "seqlevels,ChromatinAssay-method",
        "seqlevels,Seurat-method",
        "seqlevels<-,ChromatinAssay-method",
        "seqlevels<-,Seurat-method",
        "seqnames",
        "seqnames,ChromatinAssay-method",
        "seqnames,Seurat-method",
        "seqnames<-,ChromatinAssay-method",
        "seqnames<-,Seurat-method"
      ]
    },
    {
      "page": "SetMotifData",
      "title": "Set motif data",
      "concept": [
        "motifs"
      ],
      "topics": [
        "SetMotifData",
        "SetMotifData.ChromatinAssay",
        "SetMotifData.Motif",
        "SetMotifData.Seurat"
      ]
    },
    {
      "page": "SortIdents",
      "title": "Sorts cell metadata variable by similarity using hierarchical clustering",
      "concept": [
        "utilities"
      ],
      "topics": [
        "SortIdents"
      ]
    },
    {
      "page": "SplitFragments",
      "title": "Split fragment file by cell identities",
      "concept": [
        "fragments"
      ],
      "topics": [
        "SplitFragments"
      ]
    },
    {
      "page": "StringToGRanges",
      "title": "String to GRanges",
      "concept": [
        "utilities"
      ],
      "topics": [
        "StringToGRanges"
      ]
    },
    {
      "page": "subset.Fragment",
      "title": "Subset a Fragment object",
      "concept": [
        "fragments"
      ],
      "topics": [
        "subset.Fragment"
      ]
    },
    {
      "page": "subset.Motif",
      "title": "Subset a Motif object",
      "concept": [
        "motifs"
      ],
      "topics": [
        "subset.Motif",
        "[.Motif"
      ]
    },
    {
      "page": "SubsetMatrix",
      "title": "Subset matrix rows and columns",
      "concept": [
        "utilities"
      ],
      "topics": [
        "SubsetMatrix"
      ]
    },
    {
      "page": "theme_browser",
      "title": "Genome browser theme",
      "concept": [
        "visualization"
      ],
      "topics": [
        "theme_browser"
      ]
    },
    {
      "page": "TilePlot",
      "title": "Plot integration sites per cell",
      "concept": [
        "visualization"
      ],
      "topics": [
        "TilePlot"
      ]
    },
    {
      "page": "TSSEnrichment",
      "title": "Compute TSS enrichment score per cell",
      "concept": [
        "qc"
      ],
      "topics": [
        "TSSEnrichment"
      ]
    },
    {
      "page": "TSSPlot",
      "title": "Plot signal enrichment around TSSs",
      "concept": [
        "qc",
        "visualization"
      ],
      "topics": [
        "TSSPlot"
      ]
    },
    {
      "page": "UnifyPeaks",
      "title": "Unify genomic ranges",
      "concept": [
        "preprocessing",
        "utilities"
      ],
      "topics": [
        "UnifyPeaks"
      ]
    },
    {
      "page": "UpdatePath",
      "title": "Update the file path for a Fragment object",
      "concept": [
        "fragments"
      ],
      "topics": [
        "UpdatePath"
      ]
    },
    {
      "page": "ValidateCells",
      "title": "Validate cells present in fragment file",
      "concept": [
        "fragments"
      ],
      "topics": [
        "ValidateCells"
      ]
    },
    {
      "page": "ValidateFragments",
      "title": "Validate Fragment object",
      "concept": [
        "fragments"
      ],
      "topics": [
        "ValidateFragments"
      ]
    },
    {
      "page": "ValidateHash",
      "title": "Validate hashes for Fragment object",
      "concept": [
        "fragments"
      ],
      "topics": [
        "ValidateHash"
      ]
    },
    {
      "page": "VariantPlot",
      "title": "Plot strand concordance vs. VMR",
      "concept": [
        "mito",
        "visualization"
      ],
      "topics": [
        "VariantPlot"
      ]
    }
  ],
  "_pkglogo": "https://github.com/stuart-lab/signac/raw/HEAD/man/figures/logo.svg",
  "_readme": "https://github.com/stuart-lab/signac/raw/HEAD/README.md",
  "_rundeps": [
    "askpass",
    "BH",
    "BiocGenerics",
    "BiocParallel",
    "Biostrings",
    "bitops",
    "cli",
    "codetools",
    "cpp11",
    "crayon",
    "curl",
    "data.table",
    "digest",
    "dotCall64",
    "dplyr",
    "farver",
    "fastmatch",
    "formatR",
    "futile.logger",
    "futile.options",
    "future",
    "future.apply",
    "generics",
    "GenomeInfoDb",
    "GenomicRanges",
    "ggplot2",
    "globals",
    "glue",
    "gtable",
    "httr",
    "IRanges",
    "isoband",
    "jsonlite",
    "labeling",
    "lambda.r",
    "lattice",
    "lifecycle",
    "listenv",
    "magrittr",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "mime",
    "openssl",
    "parallelly",
    "patchwork",
    "pbapply",
    "pillar",
    "pkgconfig",
    "progressr",
    "purrr",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "RcppEigen",
    "RcppRoll",
    "Rhtslib",
    "rlang",
    "Rsamtools",
    "RSpectra",
    "S4Vectors",
    "S7",
    "scales",
    "Seqinfo",
    "SeuratObject",
    "snow",
    "sp",
    "spam",
    "sparseMatrixStats",
    "stringi",
    "stringr",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "UCSC.utils",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr",
    "XVector"
  ],
  "_sysdeps": [
    {
      "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"
    }
  ],
  "_score": 13.446864853218061,
  "_indexed": true,
  "_nocasepkg": "signac",
  "_universes": [
    "stuart-lab",
    "timoast"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.17.1",
      "date": "2026-05-11T09:45:03.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "12d1ff82774890b08e55b3101f36fab83e674b88",
      "fileid": "fb717079255328637c195bb0060462fdfbb6cd56ae2f74745342f4197900bb89",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/stuart-lab/actions/runs/25662218372"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.17.1",
      "date": "2026-05-11T09:44:59.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "12d1ff82774890b08e55b3101f36fab83e674b88",
      "fileid": "5072676f84b0fb2a2d36ac08b8aaab8c904d9fcd1f7624bda73ec571019c9c96",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/stuart-lab/actions/runs/25662218372"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.17.1",
      "date": "2026-05-11T09:45:07.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "12d1ff82774890b08e55b3101f36fab83e674b88",
      "fileid": "2ce1061ea1c2958749792e919f2fd22c06f9c94bf511b6fb02f3f925eaa346eb",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/stuart-lab/actions/runs/25662218372"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.17.1",
      "date": "2026-05-11T09:45:19.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "12d1ff82774890b08e55b3101f36fab83e674b88",
      "fileid": "48131b6b01d608e387d6d4d86641683cd742fc97d59d8f8fd40742b670606cf2",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/stuart-lab/actions/runs/25662218372"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.17.1",
      "date": "2026-05-11T09:43:59.000Z",
      "arch": "aarch64",
      "commit": "12d1ff82774890b08e55b3101f36fab83e674b88",
      "fileid": "d294acfcc74e3af86419d9029368aed98a82518dd6c8fc98354b6dbb05e03db0",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/stuart-lab/actions/runs/25662218372"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.17.1",
      "date": "2026-05-11T09:47:28.000Z",
      "arch": "x86_64",
      "commit": "12d1ff82774890b08e55b3101f36fab83e674b88",
      "fileid": "29bbd7543b3bec2e0f33ddbf412410190aa89981bf012a46323f6b8ffb3a62fe",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/stuart-lab/actions/runs/25662218372"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.17.1",
      "date": "2026-05-11T09:43:47.000Z",
      "arch": "aarch64",
      "commit": "12d1ff82774890b08e55b3101f36fab83e674b88",
      "fileid": "50858d62c609b941bcb87d9c863aa85233ecccc5c918dcf5a4fc2723515fff2d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/stuart-lab/actions/runs/25662218372"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.17.1",
      "date": "2026-05-11T09:45:55.000Z",
      "arch": "x86_64",
      "commit": "12d1ff82774890b08e55b3101f36fab83e674b88",
      "fileid": "b8b578990f2b537c82068d281c5c08684bbf139fa6fada776b3fdf894b2220c2",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/stuart-lab/actions/runs/25662218372"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.17.1",
      "date": "2026-05-11T09:43:38.000Z",
      "arch": "x86_64",
      "commit": "12d1ff82774890b08e55b3101f36fab83e674b88",
      "fileid": "6a3e210575aa1049a452bb9f61fdc8dd31c9428bd25b38c472b5c06d76a3c1f1",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/stuart-lab/actions/runs/25662218372"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.17.1",
      "date": "2026-05-11T09:43:56.000Z",
      "arch": "x86_64",
      "commit": "12d1ff82774890b08e55b3101f36fab83e674b88",
      "fileid": "2a094fe1b1a15a474e1a29afdef4eb5dc1a8d5a78e956fee8b8b43794146421a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/stuart-lab/actions/runs/25662218372"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.17.1",
      "date": "2026-05-11T09:43:43.000Z",
      "arch": "x86_64",
      "commit": "12d1ff82774890b08e55b3101f36fab83e674b88",
      "fileid": "5b8dae0267c2a9f376ad9a8361da0549b6307f79f84bc9daeda4b763b6b17f03",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/stuart-lab/actions/runs/25662218372"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.17.1",
      "date": "2026-05-22T11:26:32.000Z",
      "arch": "emscripten",
      "commit": "12d1ff82774890b08e55b3101f36fab83e674b88",
      "fileid": "9acb1f780194e0352df7b759da60a08e148e80781e3fecb0b8aa8ff8d0964472",
      "status": "success",
      "buildurl": "https://github.com/r-universe/stuart-lab/actions/runs/25662218372"
    }
  ]
}