{
  "_id": "6a5b39e49baadeef8ab4ccb9",
  "Package": "powerTCR",
  "Type": "Package",
  "Title": "Model-Based Comparative Analysis of the TCR Repertoire",
  "Version": "1.33.0",
  "Date": "2018-01-23",
  "Author": "Hillary Koch",
  "Maintainer": "Hillary Koch <hillary.koch01@gmail.com>",
  "Description": "This package provides a model for the clone size\ndistribution of the TCR repertoire. Further, it permits\ncomparative analysis of TCR repertoire libraries based on\ntheoretical model fits.",
  "License": "Artistic-2.0",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "VignetteBuilder": "knitr",
  "biocViews": "Software, Clustering, BiomedicalInformatics",
  "Config/pak/sysreqs": "make libgsl0-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:47:15 UTC",
  "RemoteUrl": "https://github.com/bioc/powerTCR",
  "RemoteRef": "HEAD",
  "RemoteSha": "5c4d0f2395482e1a1d70e8a34e7f139af84b0b26",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-07-18 08:26:25 UTC",
    "User": "root"
  },
  "_user": "bioc",
  "_type": "src",
  "_file": "powerTCR_1.33.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/f57d0ebaca68c4dc04cae018cf6dd61fce8eef31890bd038710515a6f7f0be40",
  "_filesize": 352802,
  "_sha256": "f57d0ebaca68c4dc04cae018cf6dd61fce8eef31890bd038710515a6f7f0be40",
  "_expires": "2026-10-26T08:31:30.000Z",
  "_created": "2026-07-18T08:26:25.000Z",
  "_published": "2026-07-18T08:31:32.419Z",
  "_bioccheck": {
    "error": 1,
    "warning": 5,
    "note": 14
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/29637369663",
  "_status": "success",
  "_upstream": "https://github.com/bioc/powerTCR",
  "_commit": {
    "id": "5c4d0f2395482e1a1d70e8a34e7f139af84b0b26",
    "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": 1777380435
  },
  "_maintainer": {
    "name": "Hillary Koch",
    "email": "hillary.koch01@gmail.com",
    "login": "hillary-koch",
    "description": "",
    "uuid": 187787978
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 88062185695,
      "time": 167,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "8427565430"
    },
    {
      "job": 88062185691,
      "time": 257,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "8427577411"
    },
    {
      "job": 88062185700,
      "time": 241,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8427575231"
    },
    {
      "job": 88062185697,
      "time": 101,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "8427556527"
    },
    {
      "job": 88062185711,
      "time": 114,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8427558274"
    },
    {
      "job": 88061961557,
      "time": 184,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8427542952"
    },
    {
      "job": 88062185704,
      "time": 114,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8427558340"
    },
    {
      "job": 88062185723,
      "time": 128,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "8427560173"
    },
    {
      "job": 88062185717,
      "time": 119,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "8427559115"
    },
    {
      "job": 88062185722,
      "time": 125,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8427559802"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "cubature",
      "role": "Imports"
    },
    {
      "package": "doParallel",
      "role": "Imports"
    },
    {
      "package": "evmix",
      "role": "Imports"
    },
    {
      "package": "foreach",
      "role": "Imports"
    },
    {
      "package": "magrittr",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "parallel",
      "role": "Imports"
    },
    {
      "package": "purrr",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "truncdist",
      "role": "Imports"
    },
    {
      "package": "vegan",
      "role": "Imports"
    },
    {
      "package": "VGAM",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "RUnit",
      "role": "Suggests"
    },
    {
      "package": "BiocGenerics",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.33.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.32.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "software",
    "clustering",
    "biomedicalinformatics"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 447,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 692,
    "source": "https://www.bioconductor.org/packages/stats/bioc/powerTCR"
  },
  "_mentions": 1,
  "_searchresults": 6,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/powerTCR.html",
    "extra/readme.html",
    "extra/readme.md",
    "LICENSE",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "clusterPlot",
    "ddiscgammagpd",
    "fdesponds",
    "fdiscgammagpd",
    "get_bootstraps",
    "get_distances",
    "get_diversity",
    "get_mle",
    "get_nllh",
    "JS_desponds",
    "JS_dist",
    "JS_spliced",
    "pdiscgammagpd",
    "qdiscgammagpd",
    "rdiscgammagpd"
  ],
  "_datasets": [
    {
      "name": "repertoires",
      "title": "Two toy examples of sample TCR repertoires.",
      "object": "repertoires",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "Accessors",
      "title": "Grab important output from a list of fits",
      "topics": [
        "get_diversity",
        "get_mle",
        "get_nllh"
      ]
    },
    {
      "page": "clusterPlot",
      "title": "Visualize hierarchical clustering of samples",
      "topics": [
        "clusterPlot"
      ]
    },
    {
      "page": "discgammagpd",
      "title": "The discrete gamma-GPD spliced threshold distribution",
      "topics": [
        "ddiscgammagpd",
        "pdiscgammagpd",
        "qdiscgammagpd",
        "rdiscgammagpd"
      ]
    },
    {
      "page": "fdesponds",
      "title": "Fit the type-I Pareto distribution as according to Desponds et al. (2016)",
      "topics": [
        "fdesponds"
      ]
    },
    {
      "page": "fdiscgammagpd",
      "title": "Fit the discrete gamma-GPD spliced threshold model",
      "topics": [
        "fdiscgammagpd"
      ]
    },
    {
      "page": "get_bootstraps",
      "title": "Get bootstrapped fits for a list of fitted models",
      "topics": [
        "get_bootstraps"
      ]
    },
    {
      "page": "get_distances",
      "title": "Compute matrix of pairwise Jensen-Shannon Distances",
      "topics": [
        "get_distances"
      ]
    },
    {
      "page": "JS_desponds",
      "title": "Compute the Jensen-Shannon distance between two fitted distributions using the Desponds model",
      "topics": [
        "JS_desponds"
      ]
    },
    {
      "page": "JS_dist",
      "title": "Compute the Jensen-Shannon distance between two model fits",
      "topics": [
        "JS_dist"
      ]
    },
    {
      "page": "JS_spliced",
      "title": "Compute the Jensen-Shannon distance between two fitted discrete gamma-GPD spliced threshold distributions",
      "topics": [
        "JS_spliced"
      ]
    },
    {
      "page": "parse",
      "title": "Load in and parse TCR data files for use by powerTCR",
      "topics": [
        "parseFile",
        "parseFolder"
      ]
    },
    {
      "page": "repertoires",
      "title": "Two toy examples of sample TCR repertoires.",
      "topics": [
        "repertoires"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/powerTCR/raw/HEAD/README.md",
  "_rundeps": [
    "cli",
    "cluster",
    "codetools",
    "cubature",
    "doParallel",
    "evd",
    "evmix",
    "foreach",
    "glue",
    "gsl",
    "iterators",
    "lattice",
    "lifecycle",
    "magrittr",
    "MASS",
    "Matrix",
    "mgcv",
    "nlme",
    "permute",
    "purrr",
    "Rcpp",
    "rlang",
    "SparseM",
    "truncdist",
    "vctrs",
    "vegan",
    "VGAM"
  ],
  "_vignettes": [
    {
      "source": "powerTCR.Rmd",
      "filename": "powerTCR.html",
      "title": "powerTCR",
      "author": "Hillary Koch",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Summary of features",
        "Fitting a model",
        "The discrete gamma-GPD spliced threshold model",
        "The Type-I Pareto model",
        "Density, distribution, and quantile functions, plus simulating data",
        "Doing comparative analysis",
        "Extracting diversity estimators",
        "Bootstrapping model fits",
        "References"
      ],
      "created": "2018-01-28 19:34:41",
      "modified": "2018-10-25 19:22:24",
      "commits": 15
    }
  ],
  "_score": 4,
  "_indexed": true,
  "_nocasepkg": "powertcr",
  "_universes": [
    "bioc",
    "hillary-koch"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.33.0",
      "date": "2026-07-18T08:29:57.000Z",
      "distro": "resolute",
      "commit": "5c4d0f2395482e1a1d70e8a34e7f139af84b0b26",
      "fileid": "https://r2.ropensci.org/137314e3d421a22f7d4615fd440059fcf292c9a9964c341805dae59c24f2ff36",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29637369663"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.33.0",
      "date": "2026-07-18T08:29:44.000Z",
      "distro": "resolute",
      "commit": "5c4d0f2395482e1a1d70e8a34e7f139af84b0b26",
      "fileid": "https://r2.ropensci.org/eca0b2e646089368da62bc19dd6b6827e70e5fefbea7979a33c237dcd9f077e5",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29637369663"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.33.0",
      "date": "2026-07-18T08:27:46.000Z",
      "commit": "5c4d0f2395482e1a1d70e8a34e7f139af84b0b26",
      "fileid": "https://r2.ropensci.org/61f33b4ee3834ea2475ef049b0beb799ca59da9fac54b76f5b9df48013d9e129",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29637369663"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.33.0",
      "date": "2026-07-18T08:27:56.000Z",
      "commit": "5c4d0f2395482e1a1d70e8a34e7f139af84b0b26",
      "fileid": "https://r2.ropensci.org/5e73b4745e915d99b4bf72122aac7f3c77806200dcf818bdca2cd11f481c9c79",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29637369663"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.33.0",
      "date": "2026-07-18T08:28:37.000Z",
      "commit": "5c4d0f2395482e1a1d70e8a34e7f139af84b0b26",
      "fileid": "https://r2.ropensci.org/7c37c05562853e94ccd5b718773ec6f5322f40d0c1610a257fa1bfb4b9d5c474",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29637369663"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.33.0",
      "date": "2026-07-18T08:27:35.000Z",
      "commit": "5c4d0f2395482e1a1d70e8a34e7f139af84b0b26",
      "fileid": "https://r2.ropensci.org/ac548b766eaad0327ccc60f8acae9900dd9513fea6fb50d38233b57c26a31f6b",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29637369663"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.33.0",
      "date": "2026-07-18T08:27:35.000Z",
      "commit": "5c4d0f2395482e1a1d70e8a34e7f139af84b0b26",
      "fileid": "https://r2.ropensci.org/8951d8aa39b936c6580c78fe99f391bae1976ce2e3c088788563395b0fb30f2f",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29637369663"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.33.0",
      "date": "2026-07-18T08:27:35.000Z",
      "commit": "5c4d0f2395482e1a1d70e8a34e7f139af84b0b26",
      "fileid": "https://r2.ropensci.org/8af7bd609804f17cbcad694d91e011dfba61e74eac03344208122bc5c906ac8c",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29637369663"
    }
  ]
}