{
  "_id": "6a30842f3efcd9bda43486ba",
  "Package": "scDblFinder",
  "Type": "Package",
  "Title": "scDblFinder",
  "Version": "1.26.4",
  "Authors@R": "c(\nperson(\"Pierre-Luc\", \"Germain\", email=\"pierre-luc.germain@hest.ethz.ch\", role=c(\"cre\",\"aut\"), comment=c(ORCID=\"0000-0003-3418-4218\")),\nperson(\"Aaron\", \"Lun\", email=\"infinite.monkeys.with.keyboards@gmail.com\", role=\"ctb\"))",
  "URL": "https://github.com/plger/scDblFinder,\nhttps://plger.github.io/scDblFinder/",
  "BugReports": "https://github.com/plger/scDblFinder/issues",
  "Description": "The scDblFinder package gathers various methods for the\ndetection and handling of doublets/multiplets in single-cell\nsequencing data (i.e. multiple cells captured within the same\ndroplet or reaction volume). It includes methods formerly found\nin the scran package, the new fast and comprehensive\nscDblFinder method, and a reimplementation of the Amulet\ndetection method for single-cell ATAC-seq.",
  "License": "GPL-3 + file LICENSE",
  "VignetteBuilder": "knitr",
  "Encoding": "UTF-8",
  "biocViews": "Preprocessing, SingleCell, RNASeq, ATACSeq",
  "Config/roxygen2/version": "8.0.0",
  "Config/pak/sysreqs": "libcairo2-dev libfontconfig1-dev libfreetype6-dev\nlibfribidi-dev libglpk-dev make libharfbuzz-dev libbz2-dev\nlibicu-dev libjpeg-dev liblzma-dev libpng-dev libtiff-dev\nlibwebp-dev libxml2-dev libssl-dev xz-utils zlib1g-dev",
  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-06-15 16:14:20 UTC",
  "RemoteUrl": "https://github.com/bioc/scDblFinder",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "ddb83ff1ddaf2b75d040d1f74a2db663d31c2587",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-15 22:28:57 UTC",
    "User": "root"
  },
  "Author": "Pierre-Luc Germain [cre, aut] (ORCID:\n<https://orcid.org/0000-0003-3418-4218>),\nAaron Lun [ctb]",
  "Maintainer": "Pierre-Luc Germain <pierre-luc.germain@hest.ethz.ch>",
  "MD5sum": "05b6b14cbfce73f872deecf4a9868b5b",
  "_user": "bioc-release",
  "_type": "src",
  "_file": "scDblFinder_1.26.4.tar.gz",
  "_fileid": "f2c7fcf449ccefa39a32fa13cef592b8b79f8626e8ca7f721c9e3083d19c1e9f",
  "_filesize": 652693,
  "_sha256": "f2c7fcf449ccefa39a32fa13cef592b8b79f8626e8ca7f721c9e3083d19c1e9f",
  "_created": "2026-06-15T22:28:57.000Z",
  "_published": "2026-06-15T23:01:03.836Z",
  "_jobs": [
    {
      "job": 81539843878,
      "time": 312,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7652573541"
    },
    {
      "job": 81539843879,
      "time": 596,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "7652651237"
    },
    {
      "job": 81539843880,
      "time": 626,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7652659534"
    },
    {
      "job": 81539843885,
      "time": 316,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "7652572592"
    },
    {
      "job": 81539843922,
      "time": 309,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7652570816"
    },
    {
      "job": 81538661008,
      "time": 475,
      "config": "source",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7652477767"
    },
    {
      "job": 81539843874,
      "time": 229,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7652546857"
    },
    {
      "job": 81539843882,
      "time": 959,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "7652755403"
    },
    {
      "job": 81539843900,
      "time": 1850,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "7653006080"
    },
    {
      "job": 81539843893,
      "time": 900,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7652738116"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 1,
    "note": 12
  },
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27580251425",
  "_status": "failure",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/scDblFinder",
  "_commit": {
    "id": "ddb83ff1ddaf2b75d040d1f74a2db663d31c2587",
    "author": "plger <pl.germain@gmail.com>",
    "committer": "plger <pl.germain@gmail.com>",
    "message": "Merge branch 'devel' into RELEASE_3_23\n",
    "time": 1781540060
  },
  "_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
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.0",
      "role": "Depends"
    },
    {
      "package": "SingleCellExperiment",
      "role": "Depends"
    },
    {
      "package": "igraph",
      "role": "Imports"
    },
    {
      "package": "Matrix",
      "role": "Imports"
    },
    {
      "package": "BiocGenerics",
      "role": "Imports"
    },
    {
      "package": "BiocParallel",
      "role": "Imports"
    },
    {
      "package": "BiocNeighbors",
      "role": "Imports"
    },
    {
      "package": "BiocSingular",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Imports"
    },
    {
      "package": "scater",
      "role": "Imports"
    },
    {
      "package": "scrapper",
      "role": "Imports"
    },
    {
      "package": "bluster",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "DelayedArray",
      "role": "Imports"
    },
    {
      "package": "xgboost",
      "version": ">= 3.1",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "MASS",
      "role": "Imports"
    },
    {
      "package": "IRanges",
      "role": "Imports"
    },
    {
      "package": "GenomicRanges",
      "role": "Imports"
    },
    {
      "package": "GenomeInfoDb",
      "role": "Imports"
    },
    {
      "package": "Rsamtools",
      "role": "Imports"
    },
    {
      "package": "rtracklayer",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "scRNAseq",
      "role": "Suggests"
    },
    {
      "package": "circlize",
      "role": "Suggests"
    },
    {
      "package": "ComplexHeatmap",
      "role": "Suggests"
    },
    {
      "package": "ggplot2",
      "role": "Suggests"
    },
    {
      "package": "dplyr",
      "role": "Suggests"
    },
    {
      "package": "viridisLite",
      "role": "Suggests"
    },
    {
      "package": "mbkmeans",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": false,
  "_usedby": 2,
  "_updates": [
    {
      "week": "2025-29",
      "n": 7
    },
    {
      "week": "2025-33",
      "n": 1
    },
    {
      "week": "2025-43",
      "n": 7
    },
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2025-51",
      "n": 1
    },
    {
      "week": "2026-07",
      "n": 11
    },
    {
      "week": "2026-21",
      "n": 3
    },
    {
      "week": "2026-22",
      "n": 2
    },
    {
      "week": "2026-23",
      "n": 3
    },
    {
      "week": "2026-25",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.27.3",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.26.2",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "preprocessing",
    "singlecell",
    "rnaseq",
    "atacseq",
    "doublets",
    "single-cell"
  ],
  "_stars": 254,
  "_contributors": [
    {
      "user": "plger",
      "count": 599,
      "uuid": 9786697
    },
    {
      "user": "ltla",
      "count": 22,
      "uuid": 8166669
    },
    {
      "user": "jwokaty",
      "count": 16,
      "uuid": 1744257
    },
    {
      "user": "nturaga",
      "count": 12,
      "uuid": 2746443
    },
    {
      "user": "csoneson",
      "count": 2,
      "uuid": 5628952
    },
    {
      "user": "xnnba1984",
      "count": 2,
      "uuid": 65501078
    },
    {
      "user": "federicomarini",
      "count": 1,
      "uuid": 7447478
    },
    {
      "user": "hpages",
      "count": 1,
      "uuid": 8810451
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 440,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 3661,
    "source": "https://www.bioconductor.org/packages/stats/bioc/scDblFinder"
  },
  "_mentions": 7,
  "_devurl": "https://github.com/plger/scdblfinder",
  "_pkgdown": "https://plger.github.io/scDblFinder/",
  "_searchresults": 2384,
  "_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/scDblFinder.html",
    "LICENSE",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/plger/scdblfinder",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "addDoublets",
    "aggregateFeatures",
    "amulet",
    "amuletFromCounts",
    "clamulet",
    "clusterStickiness",
    "computeDoubletDensity",
    "createDoublets",
    "cxds2",
    "directDblClassification",
    "doubletPairwiseEnrichment",
    "doubletThresholding",
    "fastcluster",
    "findDoubletClusters",
    "getArtificialDoublets",
    "getCellPairs",
    "getExpectedDoublets",
    "getFragmentOverlaps",
    "mockDoubletSCE",
    "plotDoubletMap",
    "plotThresholds",
    "propHomotypic",
    "recoverDoublets",
    "scDblFinder",
    "selFeatures",
    "TFIDF"
  ],
  "_help": [
    {
      "page": "addDoublets",
      "title": "addDoublets",
      "topics": [
        "addDoublets"
      ]
    },
    {
      "page": "aggregateFeatures",
      "title": "aggregateFeatures",
      "topics": [
        "aggregateFeatures"
      ]
    },
    {
      "page": "amulet",
      "title": "amulet",
      "topics": [
        "amulet"
      ]
    },
    {
      "page": "amuletFromCounts",
      "title": "amuletFromCounts",
      "topics": [
        "amuletFromCounts"
      ]
    },
    {
      "page": "clamulet",
      "title": "clamulet",
      "topics": [
        "clamulet"
      ]
    },
    {
      "page": "clusterStickiness",
      "title": "clusterStickiness",
      "topics": [
        "clusterStickiness"
      ]
    },
    {
      "page": "computeDoubletDensity",
      "title": "Compute the density of simulated doublets",
      "topics": [
        "computeDoubletDensity",
        "computeDoubletDensity,ANY-method",
        "computeDoubletDensity,SingleCellExperiment-method",
        "computeDoubletDensity,SummarizedExperiment-method"
      ]
    },
    {
      "page": "createDoublets",
      "title": "createDoublets",
      "topics": [
        "createDoublets"
      ]
    },
    {
      "page": "cxds2",
      "title": "cxds2",
      "topics": [
        "cxds2"
      ]
    },
    {
      "page": "directDblClassification",
      "title": "directClassification",
      "topics": [
        "directDblClassification"
      ]
    },
    {
      "page": "doubletPairwiseEnrichment",
      "title": "doubletPairwiseEnrichment",
      "topics": [
        "doubletPairwiseEnrichment"
      ]
    },
    {
      "page": "doubletThresholding",
      "title": "doubletThresholding",
      "topics": [
        "doubletThresholding"
      ]
    },
    {
      "page": "fastcluster",
      "title": "fastcluster",
      "topics": [
        "fastcluster"
      ]
    },
    {
      "page": "findDoubletClusters",
      "title": "Detect doublet clusters",
      "topics": [
        "findDoubletClusters",
        "findDoubletClusters,ANY-method",
        "findDoubletClusters,SingleCellExperiment-method",
        "findDoubletClusters,SummarizedExperiment-method"
      ]
    },
    {
      "page": "getArtificialDoublets",
      "title": "getArtificialDoublets",
      "topics": [
        "getArtificialDoublets"
      ]
    },
    {
      "page": "getCellPairs",
      "title": "getCellPairs",
      "topics": [
        "getCellPairs"
      ]
    },
    {
      "page": "getExpectedDoublets",
      "title": "getExpectedDoublets",
      "topics": [
        "getExpectedDoublets"
      ]
    },
    {
      "page": "getFragmentOverlaps",
      "title": "getFragmentOverlaps",
      "topics": [
        "getFragmentOverlaps"
      ]
    },
    {
      "page": "mockDoubletSCE",
      "title": "mockDoubletSCE",
      "topics": [
        "mockDoubletSCE"
      ]
    },
    {
      "page": "plotDoubletMap",
      "title": "plotDoubletMap",
      "topics": [
        "plotDoubletMap"
      ]
    },
    {
      "page": "plotThresholds",
      "title": "plotThresholds",
      "topics": [
        "plotThresholds"
      ]
    },
    {
      "page": "propHomotypic",
      "title": "propHomotypic",
      "topics": [
        "propHomotypic"
      ]
    },
    {
      "page": "recoverDoublets",
      "title": "Recover intra-sample doublets",
      "topics": [
        "recoverDoublets",
        "recoverDoublets,ANY-method",
        "recoverDoublets,SingleCellExperiment-method",
        "recoverDoublets,SummarizedExperiment-method"
      ]
    },
    {
      "page": "scDblFinder",
      "title": "scDblFinder",
      "topics": [
        "scDblFinder"
      ]
    },
    {
      "page": "selFeatures",
      "title": "selFeatures",
      "topics": [
        "selFeatures"
      ]
    },
    {
      "page": "TFIDF",
      "title": "TFIDF",
      "topics": [
        "TFIDF"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/scDblFinder/raw/RELEASE_3_23/README.md",
  "_rundeps": [
    "abind",
    "askpass",
    "assorthead",
    "base64enc",
    "beachmat",
    "beeswarm",
    "BH",
    "Biobase",
    "BiocGenerics",
    "BiocIO",
    "biocmake",
    "BiocNeighbors",
    "BiocParallel",
    "BiocSingular",
    "Biostrings",
    "bitops",
    "bluster",
    "Cairo",
    "cigarillo",
    "cli",
    "cluster",
    "codetools",
    "cpp11",
    "crayon",
    "curl",
    "data.table",
    "DelayedArray",
    "dir.expiry",
    "dqrng",
    "farver",
    "filelock",
    "FNN",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomeInfoDb",
    "GenomicAlignments",
    "GenomicRanges",
    "ggbeeswarm",
    "ggplot2",
    "ggrastr",
    "ggrepel",
    "glue",
    "gridExtra",
    "gtable",
    "httr",
    "igraph",
    "IRanges",
    "irlba",
    "isoband",
    "jsonlite",
    "labeling",
    "lambda.r",
    "lattice",
    "lifecycle",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "mime",
    "openssl",
    "pheatmap",
    "pkgconfig",
    "png",
    "R6",
    "ragg",
    "RColorBrewer",
    "Rcpp",
    "RcppAnnoy",
    "RcppEigen",
    "RcppML",
    "RcppProgress",
    "RCurl",
    "restfulr",
    "Rhtslib",
    "Rigraphlib",
    "rjson",
    "rlang",
    "Rsamtools",
    "RSpectra",
    "rsvd",
    "rtracklayer",
    "Rtsne",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "ScaledMatrix",
    "scales",
    "scater",
    "scrapper",
    "scuttle",
    "Seqinfo",
    "SingleCellExperiment",
    "sitmo",
    "snow",
    "SparseArray",
    "stringi",
    "SummarizedExperiment",
    "sys",
    "systemfonts",
    "textshaping",
    "UCSC.utils",
    "uwot",
    "vctrs",
    "vipor",
    "viridis",
    "viridisLite",
    "withr",
    "xgboost",
    "XML",
    "XVector",
    "yaml"
  ],
  "_score": 11.513057031317844,
  "_indexed": false,
  "_nocasepkg": "scdblfinder",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://bioc.r-universe.dev/scDblFinder",
  "_previous": "1.26.2",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.26.4",
      "date": "2026-06-15T22:33:44.000Z",
      "distro": "noble",
      "commit": "ddb83ff1ddaf2b75d040d1f74a2db663d31c2587",
      "fileid": "95586061bc22a37190ce4c35acd9fcbe988ec127b51fe3956b851781a475a64d",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27580251425"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.26.4",
      "date": "2026-06-15T22:34:19.000Z",
      "distro": "noble",
      "commit": "ddb83ff1ddaf2b75d040d1f74a2db663d31c2587",
      "fileid": "21d71342585231d4248f3bf5eb19ebe9523daceddf740db8a65a18b10209376e",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27580251425"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.26.4",
      "date": "2026-06-15T22:32:10.000Z",
      "commit": "ddb83ff1ddaf2b75d040d1f74a2db663d31c2587",
      "fileid": "c46697c7bd3ec5097594ca61bd62863d4d801a56c3bed03cb35d32af1186631c",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27580251425"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.26.4",
      "date": "2026-06-15T22:31:32.000Z",
      "commit": "ddb83ff1ddaf2b75d040d1f74a2db663d31c2587",
      "fileid": "086773fa54c0d9e55225a007af4d54071445ae28b26ea696ffbad9f9dd799582",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27580251425"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.26.4",
      "date": "2026-06-15T22:33:28.000Z",
      "commit": "ddb83ff1ddaf2b75d040d1f74a2db663d31c2587",
      "fileid": "12194b60f9f8c81d898fd650d75421a32e4f8038246c20a8cb6b1c8cdf42a3a1",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27580251425"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.26.4",
      "date": "2026-06-15T22:38:46.000Z",
      "commit": "ddb83ff1ddaf2b75d040d1f74a2db663d31c2587",
      "fileid": "2079c5f7b454434ee466d123a8bc4dfd278512e73a675274540b390e6e92ea46",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27580251425"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.26.4",
      "date": "2026-06-15T22:52:13.000Z",
      "commit": "ddb83ff1ddaf2b75d040d1f74a2db663d31c2587",
      "fileid": "1d4d1448bb7956cfcff169e63a956825978b979f931502d1fc0a00f1b0278347",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27580251425"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.26.4",
      "date": "2026-06-15T22:38:30.000Z",
      "commit": "ddb83ff1ddaf2b75d040d1f74a2db663d31c2587",
      "fileid": "e8bb1ff25edf283c723c3e65c9b3a701201edd54076d90109f9e59e659e94833",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27580251425"
    }
  ]
}