{
  "_id": "6ae759cd818c9e3ef6dbbf4a",
  "Package": "CellBarcode",
  "Type": "Package",
  "Title": "Cellular DNA Barcode Analysis toolkit",
  "Version": "1.19.0",
  "Authors@R": "c(\nperson(\"Wenjie\", \"Sun\", email = \"sunwjie@gmail.com\", role = c(\"cre\", \"aut\"), comment=c(ORCID=\"0000-0002-3100-2346\")),\nperson(\"Anne-Marie\", \"Lyne\", email = \"Anne-Marie.Lyne@curie.fr\", role = \"aut\"),\nperson(\"Leila\", \"Perie\", email = \"leila.perie@curie.fr\", role = \"aut\")\n)",
  "Description": "The package CellBarcode performs Cellular DNA Barcode\nanalysis. It can handle all kinds of DNA barcodes, as long as\nthe barcode is within a single sequencing read and has a\npattern that can be matched by a regular expression.\n\\code{CellBarcode} can handle barcodes with flexible lengths,\nwith or without UMI (unique molecular identifier). This tool\nalso can be used for pre-processing some amplicon data such as\nCRISPR gRNA screening, immune repertoire sequencing, and\nmetagenome data.",
  "License": "Artistic-2.0",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.3.2",
  "biocViews": "Preprocessing, QualityControl, Sequencing, CRISPR",
  "Config/testthat/edition": "3",
  "VignetteBuilder": "knitr",
  "NeedsCompilation": "yes",
  "URL": "https://wenjie1991.github.io/CellBarcode/",
  "BugReports": "https://github.com/wenjie1991/CellBarcode/issues",
  "Config/pak/sysreqs": "libbz2-dev libicu-dev libjpeg-dev liblzma-dev\nlibpng-dev xz-utils zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:57:27 UTC",
  "RemoteUrl": "https://github.com/bioc/CellBarcode",
  "RemoteRef": "HEAD",
  "RemoteSha": "20a396a3373b3c0372c317d6699e771d4515994d",
  "Packaged": {
    "Date": "2026-11-01 13:24:26 UTC",
    "User": "root"
  },
  "Author": "Wenjie Sun [cre, aut] (ORCID: <https://orcid.org/0000-0002-3100-2346>),\nAnne-Marie Lyne [aut],\nLeila Perie [aut]",
  "Maintainer": "Wenjie Sun <sunwjie@gmail.com>",
  "_user": "bioc",
  "_type": "src",
  "_file": "CellBarcode_1.19.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/8d3e60f82b90de872b49e09647aaf74d70bbebabf4b70bd9461536a3255e58b1",
  "_filesize": 2977983,
  "_sha256": "8d3e60f82b90de872b49e09647aaf74d70bbebabf4b70bd9461536a3255e58b1",
  "_expires": "2027-02-09T15:24:59.000Z",
  "_created": "2026-11-01T13:24:26.000Z",
  "_published": "2026-11-01T15:25:01.490Z",
  "_upstream": "https://github.com/bioc/CellBarcode",
  "_status": "success",
  "_maintainer": {
    "name": "Wenjie Sun",
    "email": "sunwjie@gmail.com",
    "login": "wenjie1991",
    "description": "Passion about {How} and {Why} using R, C++, HTML, JavaScript, statistics, NGS, and Love.",
    "uuid": 6602710,
    "orcid": "0000-0002-3100-2346"
  },
  "_jobs": [
    {
      "job": 124861693651,
      "time": 217,
      "config": "bioc-checks",
      "r": "4.6.2",
      "check": "WARNING",
      "artifact": "13086700670"
    },
    {
      "job": 124861693743,
      "time": 220,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "13085615854"
    },
    {
      "job": 124861693691,
      "time": 296,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "13086667027"
    },
    {
      "job": 124861693768,
      "time": 211,
      "config": "linux-release-arm64",
      "r": "4.6.2",
      "check": "WARNING",
      "artifact": "13085775827"
    },
    {
      "job": 124861693736,
      "time": 360,
      "config": "linux-release-x86_64",
      "r": "4.6.2",
      "check": "WARNING",
      "artifact": "13086597912"
    },
    {
      "job": 124861693751,
      "time": 235,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "13089740346"
    },
    {
      "job": 124861693733,
      "time": 419,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "13089327722"
    },
    {
      "job": 124861693738,
      "time": 245,
      "config": "macos-release-arm64",
      "r": "4.6.2",
      "check": "WARNING",
      "artifact": "13088922190"
    },
    {
      "job": 124861693702,
      "time": 431,
      "config": "macos-release-x86_64",
      "r": "4.6.2",
      "check": "WARNING",
      "artifact": "13089173072"
    },
    {
      "job": 124858236951,
      "time": 292,
      "config": "source",
      "r": "4.6.2",
      "check": "OK",
      "artifact": "13085004224"
    },
    {
      "job": 124861693682,
      "time": 139,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "13086517638"
    },
    {
      "job": 124861693698,
      "time": 328,
      "config": "windows-devel-arm64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "13085094895"
    },
    {
      "job": 124861693762,
      "time": 293,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "13085826160"
    },
    {
      "job": 124861693772,
      "time": 248,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "13085905937"
    },
    {
      "job": 124861693737,
      "time": 372,
      "config": "windows-release-arm64",
      "r": "4.6.2",
      "check": "WARNING",
      "artifact": "13085313804"
    },
    {
      "job": 124861693742,
      "time": 233,
      "config": "windows-release-x86_64",
      "r": "4.6.2",
      "check": "WARNING",
      "artifact": "13085582625"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 1,
    "note": 12
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/41309484909",
  "_commit": {
    "id": "20a396a3373b3c0372c317d6699e771d4515994d",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777381047
  },
  "_distro": "resolute",
  "_host": "GitHub-Actions",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.1.0",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "BH",
      "role": "LinkingTo"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "Rcpp",
      "version": ">= 1.0.5",
      "role": "Imports"
    },
    {
      "package": "data.table",
      "version": ">= 1.12.6",
      "role": "Imports"
    },
    {
      "package": "plyr",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "stringr",
      "role": "Imports"
    },
    {
      "package": "magrittr",
      "role": "Imports"
    },
    {
      "package": "ShortRead",
      "version": ">= 1.48.0",
      "role": "Imports"
    },
    {
      "package": "Biostrings",
      "version": ">= 2.58.0",
      "role": "Imports"
    },
    {
      "package": "egg",
      "role": "Imports"
    },
    {
      "package": "Ckmeans.1d.dp",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "seqinr",
      "role": "Imports"
    },
    {
      "package": "Rsamtools",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.19.0",
      "bioc": "3.24",
      "repository": "bioc"
    },
    {
      "branch": "release",
      "version": "1.18.0",
      "bioc": "3.23",
      "repository": "bioc"
    }
  ],
  "_topics": [
    "preprocessing",
    "qualitycontrol",
    "sequencing",
    "crispr",
    "amplicon",
    "amplicon-sequencing",
    "cellular-barcode",
    "cpp"
  ],
  "_stars": 3,
  "_contributors": [
    {
      "user": "wenjie1991",
      "count": 237,
      "uuid": 6602710
    },
    {
      "user": "jwokaty",
      "count": 10,
      "uuid": 1744257
    },
    {
      "user": "nturaga",
      "count": 4,
      "uuid": 2746443
    },
    {
      "user": "sanchit-saini",
      "count": 1,
      "uuid": 49326387
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 482,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 534,
    "source": "https://www.bioconductor.org/packages/stats/bioc/CellBarcode"
  },
  "_devurl": "https://github.com/wenjie1991/cellbarcode",
  "_pkgdown": "https://wenjie1991.github.io/CellBarcode/",
  "_searchresults": 13,
  "_abi": {
    "exports": [
      {
        "key": "CellBarcode::BarcodeObj",
        "hash": "d2aba75aadc2a80b"
      },
      {
        "key": "CellBarcode::BarcodeQc",
        "hash": "95ea69d080a864d7"
      },
      {
        "key": "CellBarcode::BarcodeQcSet",
        "hash": "6324a78ed08e2f57"
      },
      {
        "key": "CellBarcode::generic:bc_2df",
        "hash": "168d5b01666f7ac0"
      },
      {
        "key": "CellBarcode::generic:bc_2dt",
        "hash": "9729317939e7be69"
      },
      {
        "key": "CellBarcode::generic:bc_2matrix",
        "hash": "b6ba7fa75a17b7d1"
      },
      {
        "key": "CellBarcode::generic:bc_auto_cutoff",
        "hash": "5a9127e8b22626a4"
      },
      {
        "key": "CellBarcode::generic:bc_barcodes",
        "hash": "ccbafee55e54821f"
      },
      {
        "key": "CellBarcode::generic:bc_cleanBc",
        "hash": "e7e071a7dd8375ae"
      },
      {
        "key": "CellBarcode::generic:bc_create_BarcodeObj",
        "hash": "bf418a6563599c80"
      },
      {
        "key": "CellBarcode::generic:bc_cure_cluster",
        "hash": "8303873ab8bb7f63"
      },
      {
        "key": "CellBarcode::generic:bc_cure_depth",
        "hash": "053271e1c36a5a14"
      },
      {
        "key": "CellBarcode::generic:bc_cure_umi",
        "hash": "1aff7850ef8fbc6b"
      },
      {
        "key": "CellBarcode::generic:bc_extract",
        "hash": "52dc3dc13eeb44d9"
      },
      {
        "key": "CellBarcode::generic:bc_merge",
        "hash": "df7f4556a2776813"
      },
      {
        "key": "CellBarcode::generic:bc_messyBc",
        "hash": "2a0b5d09535502d0"
      },
      {
        "key": "CellBarcode::generic:bc_meta",
        "hash": "ad48f7ece62e2928"
      },
      {
        "key": "CellBarcode::generic:bc_meta<-",
        "hash": "dec3a4d3b54f6741"
      },
      {
        "key": "CellBarcode::generic:bc_names",
        "hash": "4ac7231aef06644b"
      },
      {
        "key": "CellBarcode::generic:bc_names<-",
        "hash": "5d229d795b5fe730"
      },
      {
        "key": "CellBarcode::generic:bc_plot_count",
        "hash": "f7d310310c11fc57"
      },
      {
        "key": "CellBarcode::generic:bc_plot_mutual",
        "hash": "e04ba6002f902f3e"
      },
      {
        "key": "CellBarcode::generic:bc_plot_pair",
        "hash": "e8615877df7f619d"
      },
      {
        "key": "CellBarcode::generic:bc_plot_seqQc",
        "hash": "7dc3467c8ac44fb8"
      },
      {
        "key": "CellBarcode::generic:bc_plot_single",
        "hash": "45f67cfb20250425"
      },
      {
        "key": "CellBarcode::generic:bc_seq_filter",
        "hash": "c48fe746d38a0ec4"
      },
      {
        "key": "CellBarcode::generic:bc_seq_qc",
        "hash": "d41642ba39637383"
      },
      {
        "key": "CellBarcode::generic:bc_subset",
        "hash": "c830fd79424e8cf2"
      },
      {
        "key": "CellBarcode::generic:bc_summary_barcode",
        "hash": "f71723c505c9bd2a"
      },
      {
        "key": "CellBarcode::generic:bc_summary_seqQc",
        "hash": "fc43af4178f91216"
      },
      {
        "key": "CellBarcode::listOrNull",
        "hash": "9d744ab8b72ddd3a"
      }
    ],
    "imports": [
      {
        "key": "Rcpp::Rcpp_precious_preserve()",
        "hash": "33a97ea62b293da6"
      },
      {
        "key": "Rcpp::Rcpp_precious_remove()",
        "hash": "63d26947ba7e1377"
      },
      {
        "key": "Rcpp::char_get_string_elt()",
        "hash": "b8ef75689d832a84"
      },
      {
        "key": "Rcpp::dataptr()",
        "hash": "54e69ad2e6668c83"
      },
      {
        "key": "Rcpp::demangle()",
        "hash": "b0cfd6754c5ebc4e"
      },
      {
        "key": "Rcpp::enterRNGScope()",
        "hash": "a04a299137cef947"
      },
      {
        "key": "Rcpp::exitRNGScope()",
        "hash": "a04a299137cef947"
      },
      {
        "key": "Rcpp::rcpp_get_stack_trace()",
        "hash": "c684a9bbe15cdc52"
      },
      {
        "key": "Rcpp::rcpp_set_stack_trace()",
        "hash": "33a97ea62b293da6"
      }
    ]
  },
  "_rbuild": "4.6.2",
  "_assets": [
    "extra/CellBarcode.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/wenjie1991/cellbarcode",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "bc_2df",
    "bc_2dt",
    "bc_2matrix",
    "bc_auto_cutoff",
    "bc_barcodes",
    "bc_cleanBc",
    "bc_create_BarcodeObj",
    "bc_cure_cluster",
    "bc_cure_depth",
    "bc_cure_umi",
    "bc_extract",
    "bc_extract_sc_bam",
    "bc_extract_sc_fastq",
    "bc_extract_sc_sam",
    "bc_merge",
    "bc_messyBc",
    "bc_meta",
    "bc_meta<-",
    "bc_names",
    "bc_names<-",
    "bc_plot_count",
    "bc_plot_mutual",
    "bc_plot_pair",
    "bc_plot_seqQc",
    "bc_plot_single",
    "bc_seq_filter",
    "bc_seq_qc",
    "bc_splitVDJ",
    "bc_subset",
    "bc_summary_barcode",
    "bc_summary_seqQc",
    "format",
    "show"
  ],
  "_datasets": [
    {
      "name": "bc_obj",
      "title": "A dummy BarcodeObj object",
      "object": "bc_obj",
      "file": "bc_obj.RData",
      "class": [
        "BarcodeObj"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "BarcodeObj",
      "title": "BarcodeObj object",
      "topics": [
        "BarcodeObj",
        "BarcodeObj-class"
      ]
    },
    {
      "page": "bc_2df",
      "title": "Transforms BarcodeObj object into another data type",
      "topics": [
        "bc_2df",
        "bc_2df,BarcodeObj-method",
        "bc_2dt",
        "bc_2dt,BarcodeObj-method",
        "bc_2matrix",
        "bc_2matrix,BarcodeObj-method"
      ]
    },
    {
      "page": "bc_auto_cutoff",
      "title": "Finds barcode count cutoff point",
      "topics": [
        "bc_auto_cutoff",
        "bc_auto_cutoff,BarcodeObj-method"
      ]
    },
    {
      "page": "bc_barcodes",
      "title": "Gets barcode sequences",
      "topics": [
        "bc_barcodes",
        "bc_barcodes,BarcodeObj-method"
      ]
    },
    {
      "page": "bc_cleanBc",
      "title": "Accesses cleanBc slot in the BarcodeObj object",
      "topics": [
        "bc_cleanBc",
        "bc_cleanBc,BarcodeObj-method"
      ]
    },
    {
      "page": "bc_create_BarcodeObj",
      "title": "Create a BarcodeObj object from extracted barcodes data",
      "topics": [
        "bc_create_BarcodeObj",
        "bc_create_BarcodeObj,data.frame-method",
        "bc_create_BarcodeObj,matrix-method"
      ]
    },
    {
      "page": "bc_cure_cluster",
      "title": "Clean barcodes by editing distance",
      "topics": [
        "bc_cure_cluster",
        "bc_cure_cluster,BarcodeObj-method"
      ]
    },
    {
      "page": "bc_cure_depth",
      "title": "Filters barcodes by counts",
      "topics": [
        "bc_cure_depth",
        "bc_cure_depth,BarcodeObj-method"
      ]
    },
    {
      "page": "bc_cure_umi",
      "title": "Filters UMI-barcode tag by counts",
      "topics": [
        "bc_cure_umi",
        "bc_cure_umi,BarcodeObj-method"
      ]
    },
    {
      "page": "bc_extract",
      "title": "Extract barcode from sequences",
      "topics": [
        "bc_extract",
        "bc_extract,character-method",
        "bc_extract,data.frame-method",
        "bc_extract,DNAStringSet-method",
        "bc_extract,integer-method",
        "bc_extract,list-method",
        "bc_extract,ShortReadQ-method"
      ]
    },
    {
      "page": "bc_extract_sc_fastq",
      "title": "Extract barcode from single-cell sequencing fastq file",
      "topics": [
        "bc_extract_sc_fastq"
      ]
    },
    {
      "page": "bc_extract_sc_sam",
      "title": "Extract barcode from single-cell sequencing sam file",
      "topics": [
        "bc_extract_sc_bam",
        "bc_extract_sc_sam"
      ]
    },
    {
      "page": "bc_messyBc",
      "title": "Accesses messyBc slot in the BarcodeObj object",
      "topics": [
        "bc_messyBc",
        "bc_messyBc,BarcodeObj-method"
      ]
    },
    {
      "page": "bc_meta",
      "title": "Accesses and sets metadata in BarcodeObj object",
      "topics": [
        "bc_meta",
        "bc_meta,BarcodeObj-method",
        "bc_meta<-",
        "bc_meta<-,BarcodeObj-method"
      ]
    },
    {
      "page": "bc_names",
      "title": "Access & update sample names in BarcodeObj & and BarcodeQcSet",
      "topics": [
        "bc_names",
        "bc_names,BarcodeObj-method",
        "bc_names,BarcodeQcSet-method",
        "bc_names<-",
        "bc_names<-,BarcodeObj,character-method",
        "bc_names<-,BarcodeQcSet,ANY-method"
      ]
    },
    {
      "page": "bc_obj",
      "title": "A dummy BarcodeObj object",
      "topics": [
        "bc_obj"
      ]
    },
    {
      "page": "bc_plot_count",
      "title": "Plot for counts distribution",
      "topics": [
        "bc_plot_count",
        "bc_plot_count,BarcodeObj-method"
      ]
    },
    {
      "page": "bc_plot_mutual",
      "title": "Barcode read count 2D scatter plot of sample combination",
      "topics": [
        "bc_plot_mutual",
        "bc_plot_mutual,BarcodeObj-method"
      ]
    },
    {
      "page": "bc_plot_pair",
      "title": "Barcode read count 2D scatter plot for given pairs",
      "topics": [
        "bc_plot_pair",
        "bc_plot_pair,BarcodeObj-method"
      ]
    },
    {
      "page": "bc_plot_single",
      "title": "Scatter plot of barcode count distribution per sample",
      "topics": [
        "bc_plot_single",
        "bc_plot_single,BarcodeObj-method"
      ]
    },
    {
      "page": "bc_seq_filter",
      "title": "Remove low-quality sequence",
      "topics": [
        "bc_seq_filter",
        "bc_seq_filter,character-method",
        "bc_seq_filter,data.frame-method",
        "bc_seq_filter,DNAStringSet-method",
        "bc_seq_filter,integer-method",
        "bc_seq_filter,list-method",
        "bc_seq_filter,ShortReadQ-method"
      ]
    },
    {
      "page": "bc_seq_qc",
      "title": "Evaluates sequences quality",
      "topics": [
        "BarcodeQc",
        "BarcodeQc-class",
        "BarcodeQcSet",
        "BarcodeQcSet-class",
        "bc_plot_seqQc",
        "bc_plot_seqQc,BarcodeQc-method",
        "bc_plot_seqQc,BarcodeQcSet-method",
        "bc_seq_qc",
        "bc_seq_qc,character-method",
        "bc_seq_qc,data.frame-method",
        "bc_seq_qc,DNAStringSet-method",
        "bc_seq_qc,integer-method",
        "bc_seq_qc,list-method",
        "bc_seq_qc,ShortReadQ-method"
      ]
    },
    {
      "page": "bc_splitVDJ",
      "title": "Parse VDJ recombination (experimental)",
      "topics": [
        "bc_splitVDJ"
      ]
    },
    {
      "page": "bc_subset",
      "title": "Manages barcodes and samples in a BarcodeObj object",
      "topics": [
        "*.BarcodeObj",
        "+.BarcodeObj",
        "-.BarcodeObj",
        "bc_merge",
        "bc_merge,BarcodeObj,BarcodeObj-method",
        "bc_subset",
        "bc_subset,BarcodeObj-method"
      ]
    },
    {
      "page": "bc_summary_barcode",
      "title": "Summary and evaluate barcode diversity",
      "topics": [
        "bc_summary_barcode",
        "bc_summary_barcode,BarcodeObj-method"
      ]
    },
    {
      "page": "bc_summary_seqQc",
      "title": "Summary barcodeQcSet",
      "topics": [
        "bc_summary_seqQc",
        "bc_summary_seqQc,BarcodeQcSet-method"
      ]
    },
    {
      "page": "CellBarcode",
      "title": "DNA Barcode Analysis toolkit",
      "topics": [
        "CellBarcode-package",
        "CellBarcode"
      ]
    },
    {
      "page": "format",
      "title": "Formats BarcodeObj object",
      "topics": [
        "format,BarcodeObj-method"
      ]
    },
    {
      "page": "parse_10x_sam",
      "title": "Parse 10X bam file",
      "topics": [
        "parse_10x_sam"
      ]
    },
    {
      "page": "seq_correct",
      "title": "Sequence clustering",
      "topics": [
        "seq_correct"
      ]
    },
    {
      "page": "show",
      "title": "Show BarcodeObj object",
      "topics": [
        "show,BarcodeObj-method",
        "show,BarcodeQc-method",
        "show,BarcodeQcSet-method"
      ]
    },
    {
      "page": "subset",
      "title": "Subset the BarcodeQcSet",
      "topics": [
        "subset,BarcodeQcSet-method",
        "[,BarcodeQcSet,ANY,ANY,ANY-method"
      ]
    }
  ],
  "_pkglogo": "https://github.com/bioc/CellBarcode/raw/HEAD/logo.png",
  "_readme": "https://github.com/bioc/CellBarcode/raw/HEAD/README.md",
  "_rundeps": [
    "ade4",
    "BH",
    "Biobase",
    "BiocGenerics",
    "BiocParallel",
    "Biostrings",
    "bitops",
    "cigarillo",
    "Ckmeans.1d.dp",
    "cli",
    "codetools",
    "cpp11",
    "crayon",
    "data.table",
    "deldir",
    "egg",
    "farver",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicAlignments",
    "GenomicRanges",
    "ggplot2",
    "glue",
    "gridExtra",
    "gtable",
    "hwriter",
    "interp",
    "IRanges",
    "isoband",
    "jpeg",
    "labeling",
    "lambda.r",
    "lattice",
    "latticeExtra",
    "lifecycle",
    "magrittr",
    "MASS",
    "nlme",
    "pixmap",
    "plyr",
    "png",
    "pwalign",
    "R6",
    "rbibutils",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "RcppEigen",
    "Rdpack",
    "Rhtslib",
    "rlang",
    "Rsamtools",
    "S4Vectors",
    "S7",
    "scales",
    "segmented",
    "Seqinfo",
    "seqinr",
    "ShortRead",
    "snow",
    "sp",
    "stringi",
    "stringr",
    "vctrs",
    "viridisLite",
    "withr",
    "XVector"
  ],
  "_sysdeps": [
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "16-20260322-1ubuntu1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    }
  ],
  "_vignettes": [
    {
      "source": "Barcode_in_10X_scRNASeq.Rmd",
      "filename": "Barcode_in_10X_scRNASeq.html",
      "title": "Get barcode from 10X Genomics scRNASeq data",
      "author": "Wenjie Sun",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Process single cell sequencing data",
        "Preprocess of CellRanger output bam file",
        "Extract lineage barcode",
        "More about the pattern",
        "Session Info"
      ],
      "created": "2022-10-10 11:45:49",
      "modified": "2024-02-19 22:42:55",
      "commits": 3
    },
    {
      "source": "UMI_VDJ_Barcode.Rmd",
      "filename": "UMI_VDJ_Barcode.html",
      "title": "Analyzing Cellular DNA Barcode with CellBarcode",
      "author": "Wenjie Sun, Anne-Marie Lyne",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "About the package",
        "About function naming",
        "About test data set",
        "Installation",
        "A basic workflow",
        "Sequence quality control",
        "Evaluation",
        "Filtering",
        "Parse reads",
        "Sequencing without UMI",
        "Sequencing with UMI",
        "Metadata updated",
        "Data management",
        "Barcode filtering",
        "Filter UMI-barcode tag",
        "Filter by count",
        "Cluster barcode by sequence similarity",
        "Barcode count distribution",
        "Single sample",
        "Pairwise",
        "Miscellaneous",
        "Sample names",
        "Output to data.frame",
        "Output to matrix",
        "More",
        "Session Info"
      ],
      "created": "2021-03-19 14:39:18",
      "modified": "2022-10-10 11:45:49",
      "commits": 21
    }
  ],
  "_score": 5.369215857410143,
  "_indexed": true,
  "_nocasepkg": "cellbarcode",
  "_universes": [
    "bioc",
    "wenjie1991"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.19.0",
      "date": "2026-11-01T13:29:44.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "20a396a3373b3c0372c317d6699e771d4515994d",
      "fileid": "https://r2.ropensci.org/ce5cf3caed3ebba674858812985f414950c1d9f7a2e2ea213fb5464ae8cf2e89",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41309484909"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.19.0",
      "date": "2026-11-01T13:58:33.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "20a396a3373b3c0372c317d6699e771d4515994d",
      "fileid": "https://r2.ropensci.org/6c4b79531961960a4778f7c344cabd49233952db887e5c6a137d2c33649ccb6e",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41309484909"
    },
    {
      "r": "4.6.2",
      "os": "linux",
      "version": "1.19.0",
      "date": "2026-11-01T13:29:47.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "20a396a3373b3c0372c317d6699e771d4515994d",
      "fileid": "https://r2.ropensci.org/8eb608b621dc5fbe3114b83f732966ae246e3d0a92794bf8c8761c72cad14476",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41309484909"
    },
    {
      "r": "4.6.2",
      "os": "linux",
      "version": "1.19.0",
      "date": "2026-11-01T13:58:57.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "20a396a3373b3c0372c317d6699e771d4515994d",
      "fileid": "https://r2.ropensci.org/43547a27a2c898d5a375e9b4d5bfeae461534fe8a389f464c92b993440605258",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41309484909"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.19.0",
      "date": "2026-11-01T15:19:42.000Z",
      "arch": "aarch64",
      "commit": "20a396a3373b3c0372c317d6699e771d4515994d",
      "fileid": "https://r2.ropensci.org/29b3f696336cc66a9d5adc957cba23d689018fbe0dd1711e15a5e73e20f8649d",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41309484909"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.19.0",
      "date": "2026-11-01T15:20:28.000Z",
      "arch": "x86_64",
      "commit": "20a396a3373b3c0372c317d6699e771d4515994d",
      "fileid": "https://r2.ropensci.org/b2456cce8cb335033c61a967daf27f206497a54e23f3b770c79d287f84419edd",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41309484909"
    },
    {
      "r": "4.6.2",
      "os": "mac",
      "version": "1.19.0",
      "date": "2026-11-01T15:19:34.000Z",
      "arch": "aarch64",
      "commit": "20a396a3373b3c0372c317d6699e771d4515994d",
      "fileid": "https://r2.ropensci.org/e81800840bd06c0c11bc7be8e1171d96496869fc6b7114b54348eeb6cfa119c4",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41309484909"
    },
    {
      "r": "4.6.2",
      "os": "mac",
      "version": "1.19.0",
      "date": "2026-11-01T15:19:44.000Z",
      "arch": "x86_64",
      "commit": "20a396a3373b3c0372c317d6699e771d4515994d",
      "fileid": "https://r2.ropensci.org/e1c905508429c65a43db81b9baff81418675120e251f4a37112bca9b0dee4a2b",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41309484909"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.19.0",
      "date": "2026-11-01T13:57:21.000Z",
      "arch": "emscripten",
      "commit": "20a396a3373b3c0372c317d6699e771d4515994d",
      "fileid": "https://r2.ropensci.org/9c13c77e645f8cc4153149db0ec06380733e25e49d1f3bf68552219f024bdf7b",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41309484909"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.19.0",
      "date": "2026-11-01T13:28:24.000Z",
      "arch": "aarch64",
      "commit": "20a396a3373b3c0372c317d6699e771d4515994d",
      "fileid": "https://r2.ropensci.org/73108aa676c91a380686211ffa8e4d58675a064d3cb477ce7db86753ef7f7cba",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41309484909"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.19.0",
      "date": "2026-11-01T13:35:48.000Z",
      "arch": "x86_64",
      "commit": "20a396a3373b3c0372c317d6699e771d4515994d",
      "fileid": "https://r2.ropensci.org/10d2d20fa0b8772e3b7ebe6f45a27ff9d82b56b4f65ff86deb424c3e8ff72972",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41309484909"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.19.0",
      "date": "2026-11-01T13:35:36.000Z",
      "arch": "x86_64",
      "commit": "20a396a3373b3c0372c317d6699e771d4515994d",
      "fileid": "https://r2.ropensci.org/29e2b0ae3962a5de4453e2f040e71ad01a2e134b59f91a5b012b2584f11db0c4",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41309484909"
    },
    {
      "r": "4.6.2",
      "os": "win",
      "version": "1.19.0",
      "date": "2026-11-01T13:29:32.000Z",
      "arch": "aarch64",
      "commit": "20a396a3373b3c0372c317d6699e771d4515994d",
      "fileid": "https://r2.ropensci.org/988356dee57b282a4b6806fca5fdb01e4d124944f64e3f5519393cb59fbac632",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41309484909"
    },
    {
      "r": "4.6.2",
      "os": "win",
      "version": "1.19.0",
      "date": "2026-11-01T13:35:34.000Z",
      "arch": "x86_64",
      "commit": "20a396a3373b3c0372c317d6699e771d4515994d",
      "fileid": "https://r2.ropensci.org/d8c82ddabe9852c68d0e78448f4c4657fa2f8a6d770151f9d68c9d6a9e3c9392",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41309484909"
    }
  ]
}