{
  "_id": "6ac92202de46216d5edd9f5a",
  "Package": "tigger",
  "Type": "Package",
  "Version": "1.2.0.999",
  "Date": "2026-10-09",
  "Authors@R": "c(person(\"Daniel\", \"Gadala-Maria\", role=c(\"aut\"), \nemail=\"daniel.gadala-maria@yale.edu\"),\nperson(\"Susanna\", \"Marquez\", role=c(\"aut\", \"cre\"),\nemail=\"susanna.marquez@yale.edu\"),\nperson(\"Moriah\", \"Cohen\", role=c(\"aut\"),\nemail=\"moriah.cohen@biu.ac.il\"),\nperson(\"Ayelet\", \"Peres\", role=c(\"aut\"),\nemail=\"ayelet.peres@yale.edu\"),\nperson(\"Jason\", \"Vander Heiden\", role=c(\"aut\"),\nemail=\"jason.vanderheiden@gmail.com\"),\nperson(\"Gur\", \"Yaari\", role=c(\"aut\"),\nemail=\"gur.yaari@yale.edu\"),\nperson(\"Steven\", \"Kleinstein\", role=c(\"aut\", \"cph\"),\nemail=\"steven.kleinstein@yale.edu\"))",
  "Title": "Infers Novel Immunoglobulin Alleles from Sequencing Data",
  "Description": "Infers the V genotype of an individual from immunoglobulin\n(Ig) repertoire sequencing data (AIRR-Seq, Rep-Seq). Includes\ndetection of any novel alleles. This information is then used\nto correct existing V allele calls from among the sample\nsequences. Citations: Gadala-Maria, et al (2015)\n<doi:10.1073/pnas.1417683112>, Gadala-Maria, et al (2019)\n<doi:10.3389/fimmu.2019.00129>.",
  "License": "AGPL-3",
  "URL": "https://tigger.readthedocs.io",
  "BugReports": "https://github.com/immcantation/tigger/issues",
  "LazyData": "true",
  "BuildVignettes": "true",
  "VignetteBuilder": "knitr",
  "Encoding": "UTF-8",
  "Config/roxygen2/version": "8.1.0",
  "Config/pak/sysreqs": "libglpk-dev libbz2-dev libicu-dev liblzma-dev\nlibxml2-dev libx11-dev xz-utils zlib1g-dev",
  "Repository": "https://immcantation.r-universe.dev",
  "Date/Publication": "2026-10-09 11:43:49 UTC",
  "RemoteUrl": "https://github.com/immcantation/tigger",
  "RemoteRef": "HEAD",
  "RemoteSha": "2a5ef57a6d6c66691f2aaa43de174073bed9a90e",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-09 16:44:54 UTC",
    "User": "root"
  },
  "Author": "Daniel Gadala-Maria [aut],\nSusanna Marquez [aut, cre],\nMoriah Cohen [aut],\nAyelet Peres [aut],\nJason Vander Heiden [aut],\nGur Yaari [aut],\nSteven Kleinstein [aut, cph]",
  "Maintainer": "Susanna Marquez <susanna.marquez@yale.edu>",
  "_user": "immcantation",
  "_type": "src",
  "_file": "tigger_1.2.0.999.tar.gz",
  "_fileid": "https://r2.ropensci.org/fe9345dfea0e26990b975474bd45a544ebc881b16d22a961601f752a09499b71",
  "_filesize": 2961546,
  "_sha256": "fe9345dfea0e26990b975474bd45a544ebc881b16d22a961601f752a09499b71",
  "_expires": "2027-01-17T17:18:55.000Z",
  "_created": "2026-10-09T16:44:54.000Z",
  "_published": "2026-10-09T17:18:58.173Z",
  "_buildurl": "https://github.com/r-universe/immcantation/actions/runs/37960805525",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_jobs": [
    {
      "job": 113924934735,
      "time": 242,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "11632610156"
    },
    {
      "job": 113924934965,
      "time": 241,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "11632215546"
    },
    {
      "job": 113924934954,
      "time": 175,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "11633430662"
    },
    {
      "job": 113924934727,
      "time": 180,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "11632958241"
    },
    {
      "job": 113922958191,
      "time": 289,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11631049554"
    },
    {
      "job": 113924934637,
      "time": 155,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "11631209998"
    },
    {
      "job": 113924935084,
      "time": 179,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "11632475208"
    },
    {
      "job": 113924934916,
      "time": 183,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "11631755581"
    },
    {
      "job": 113924934808,
      "time": 167,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "11631810546"
    }
  ],
  "_upstream": "https://github.com/immcantation/tigger",
  "_commit": {
    "id": "2a5ef57a6d6c66691f2aaa43de174073bed9a90e",
    "author": "github-actions[bot] <github-actions[bot]@users.noreply.github.com>",
    "committer": "github-actions[bot] <github-actions[bot]@users.noreply.github.com>",
    "message": "[skip ci] Auto-render docs.\n",
    "time": 1791546229
  },
  "_maintainer": {
    "name": "Susanna Marquez",
    "email": "susanna.marquez@yale.edu",
    "login": "ssnn-airr",
    "description": "",
    "uuid": 20683719
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.0",
      "role": "Depends"
    },
    {
      "package": "ggplot2",
      "version": ">= 3.4.0",
      "role": "Depends"
    },
    {
      "package": "alakazam",
      "version": ">= 1.5.0",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "version": ">= 1.0.0",
      "role": "Imports"
    },
    {
      "package": "doParallel",
      "role": "Imports"
    },
    {
      "package": "foreach",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "gridExtra",
      "role": "Imports"
    },
    {
      "package": "gtools",
      "role": "Imports"
    },
    {
      "package": "iterators",
      "role": "Imports"
    },
    {
      "package": "lazyeval",
      "role": "Imports"
    },
    {
      "package": "parallel",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "stringi",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "version": ">= 1.1.0",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    }
  ],
  "_owner": "immcantation",
  "_selfowned": true,
  "_usedby": 2,
  "_updates": [
    {
      "week": "2026-02",
      "n": 8
    },
    {
      "week": "2026-09",
      "n": 1
    },
    {
      "week": "2026-11",
      "n": 2
    },
    {
      "week": "2026-14",
      "n": 14
    },
    {
      "week": "2026-16",
      "n": 6
    },
    {
      "week": "2026-30",
      "n": 3
    },
    {
      "week": "2026-31",
      "n": 1
    },
    {
      "week": "2026-40",
      "n": 5
    },
    {
      "week": "2026-41",
      "n": 9
    }
  ],
  "_tags": [
    {
      "name": "1.1.2",
      "date": "2026-01-09"
    },
    {
      "name": "1.1.3",
      "date": "2026-04-13"
    },
    {
      "name": "1.2.0",
      "date": "2026-10-06"
    }
  ],
  "_stars": 0,
  "_contributors": [
    {
      "user": "ssnn-airr",
      "count": 342,
      "uuid": 20683719
    },
    {
      "user": "javh",
      "count": 106,
      "uuid": 4105629
    },
    {
      "user": "ayeletperes",
      "count": 9,
      "uuid": 26592225
    },
    {
      "user": "eba28",
      "count": 7,
      "uuid": 43794704
    },
    {
      "user": "julianqz",
      "count": 3,
      "uuid": 7434521
    },
    {
      "user": "gyaari",
      "count": 1,
      "uuid": 9129835
    },
    {
      "user": "moriahco",
      "count": 1,
      "uuid": 27758534
    }
  ],
  "_userbio": {
    "uuid": 52156905,
    "type": "organization",
    "name": "Immcantation",
    "followers": 26
  },
  "_downloads": {
    "count": 706,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/tigger"
  },
  "_devurl": "https://github.com/immcantation/tigger",
  "_searchresults": 222,
  "_rbuild": "4.6.1",
  "_assets": [
    "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",
    "extra/tigger.html"
  ],
  "_homeurl": "https://github.com/immcantation/tigger",
  "_realowner": "immcantation",
  "_cranurl": true,
  "_releases": [
    {
      "version": "0.2.5",
      "date": "2016-06-08"
    },
    {
      "version": "0.2.7",
      "date": "2016-07-24"
    },
    {
      "version": "0.2.8",
      "date": "2016-08-28"
    },
    {
      "version": "0.2.9.999",
      "date": "2017-05-16"
    },
    {
      "version": "0.2.10",
      "date": "2017-07-03"
    },
    {
      "version": "0.2.11",
      "date": "2017-09-21"
    },
    {
      "version": "0.3.0",
      "date": "2018-10-03"
    },
    {
      "version": "0.3.1",
      "date": "2018-10-19"
    },
    {
      "version": "0.4.0",
      "date": "2019-07-19"
    },
    {
      "version": "1.0.0",
      "date": "2020-05-13"
    },
    {
      "version": "1.0.1",
      "date": "2022-09-20"
    },
    {
      "version": "1.1.0",
      "date": "2023-10-10"
    },
    {
      "version": "1.1.2",
      "date": "2026-01-10"
    },
    {
      "version": "1.1.3",
      "date": "2026-04-17"
    },
    {
      "version": "1.2.0",
      "date": "2026-10-06"
    }
  ],
  "_exports": [
    "cleanSeqs",
    "findNovelAlleles",
    "findUnmutatedCalls",
    "generateEvidence",
    "genotypeFasta",
    "getMutatedPositions",
    "getMutCount",
    "getPopularMutationCount",
    "inferGenotype",
    "inferGenotypeBayesian",
    "insertPolymorphisms",
    "plotGenotype",
    "plotGenotypeConfidence",
    "plotNovel",
    "readIgFasta",
    "reassignAlleles",
    "selectNovel",
    "sortAlleles",
    "subsampleDb",
    "updateAlleleNames",
    "writeFasta"
  ],
  "_datasets": [
    {
      "name": "AIRRDb",
      "title": "",
      "object": "airrDb",
      "class": [
        "spec_tbl_df",
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "sequence_id",
        "sequence",
        "rev_comp",
        "productive",
        "v_call",
        "d_call",
        "j_call",
        "sequence_alignment",
        "germline_alignment",
        "junction",
        "junction_aa",
        "v_cigar",
        "d_cigar",
        "j_cigar",
        "vj_in_frame",
        "stop_codon",
        "v_germline_end",
        "np1_length",
        "np2_length",
        "j_germline_end",
        "junction_length",
        "mutated_invariant",
        "indels",
        "d_5_trim",
        "d_3_trim",
        "j_5_trim"
      ],
      "rows": 17559,
      "table": true,
      "tojson": true
    },
    {
      "name": "GermlineIGHV",
      "title": "",
      "object": "GermlineIGHV",
      "class": [
        "character"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "SampleDb",
      "title": "",
      "object": "SampleDb",
      "class": [
        "data.frame"
      ],
      "fields": [
        "SEQUENCE_ID",
        "SEQUENCE_INPUT",
        "FUNCTIONAL",
        "IN_FRAME",
        "STOP",
        "MUTATED_INVARIANT",
        "INDELS",
        "V_CALL",
        "D_CALL",
        "J_CALL",
        "SEQUENCE_IMGT",
        "V_GERM_LENGTH_IMGT",
        "NP1_LENGTH",
        "D_5_TRIM",
        "D_3_TRIM",
        "NP2_LENGTH",
        "J_5_TRIM",
        "J_GERM_LENGTH",
        "JUNCTION_LENGTH",
        "JUNCTION"
      ],
      "rows": 17559,
      "table": true,
      "tojson": true
    },
    {
      "name": "SampleGenotype",
      "title": "",
      "object": "SampleGenotype",
      "class": [
        "data.frame"
      ],
      "fields": [
        "gene",
        "alleles",
        "counts",
        "total",
        "note"
      ],
      "rows": 9,
      "table": true,
      "tojson": true
    },
    {
      "name": "SampleGermlineIGHV",
      "title": "",
      "object": "SampleGermlineIGHV",
      "class": [
        "character"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "SampleNovel",
      "title": "",
      "object": "SampleNovel",
      "class": [
        "data.frame"
      ],
      "fields": [
        "germline_call",
        "note",
        "polymorphism_call",
        "nt_substitutions",
        "novel_imgt",
        "novel_imgt_count",
        "novel_imgt_unique_j",
        "novel_imgt_unique_cdr3",
        "perfect_match_count",
        "perfect_match_freq",
        "germline_call_count",
        "germline_call_freq",
        "mut_min",
        "mut_max",
        "mut_pass_count",
        "germline_imgt",
        "germline_imgt_count",
        "pos_min",
        "pos_max",
        "y_intercept",
        "y_intercept_pass",
        "snp_pass",
        "unmutated_count",
        "unmutated_freq",
        "unmutated_snp_j_gene_length_count",
        "snp_min_seqs_j_max_pass",
        "alpha",
        "min_seqs",
        "j_max",
        "min_frac"
      ],
      "rows": 12,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [],
  "_readme": "https://github.com/immcantation/tigger/raw/HEAD/README.md",
  "_rundeps": [
    "ade4",
    "airr",
    "alakazam",
    "ape",
    "BH",
    "BiocGenerics",
    "BiocParallel",
    "Biostrings",
    "bit",
    "bit64",
    "bitops",
    "cigarillo",
    "cli",
    "clipr",
    "codetools",
    "cpp11",
    "crayon",
    "digest",
    "doParallel",
    "dplyr",
    "farver",
    "foreach",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicAlignments",
    "GenomicRanges",
    "ggplot2",
    "glue",
    "gridExtra",
    "gtable",
    "gtools",
    "hms",
    "igraph",
    "IRanges",
    "isoband",
    "iterators",
    "jsonlite",
    "labeling",
    "lambda.r",
    "lattice",
    "lazyeval",
    "lifecycle",
    "magrittr",
    "MASS",
    "Matrix",
    "nlme",
    "pillar",
    "pixmap",
    "pkgconfig",
    "prettyunits",
    "progress",
    "purrr",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "readr",
    "Rhtslib",
    "rlang",
    "Rsamtools",
    "S4Vectors",
    "S7",
    "scales",
    "segmented",
    "Seqinfo",
    "seqinr",
    "snow",
    "sp",
    "stringi",
    "stringr",
    "tibble",
    "tidyr",
    "tidyselect",
    "tzdb",
    "utf8",
    "vctrs",
    "viridisLite",
    "vroom",
    "withr",
    "XVector",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "Tigger-Vignette.Rmd",
      "filename": "Tigger-Vignette.html",
      "title": "Tool for Immunoglobulin Genotype Elucidation via Rep-Seq (TIgGER)",
      "author": "Daniel Gadala-Maria",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Input",
        "Novel allele detection",
        "Inferring genotypes",
        "Frequency genotyping approach",
        "Bayesian genotyping approach",
        "Correcting allele calls",
        "Evidence",
        "References"
      ],
      "created": "2015-02-04 22:12:54",
      "modified": "2026-10-06 15:49:12",
      "commits": 49
    }
  ],
  "_score": 7.5558679889932705,
  "_indexed": true,
  "_nocasepkg": "tigger",
  "_universes": [
    "immcantation",
    "ssnn-airr"
  ],
  "_previous": "1.2.0",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.2.0.999",
      "date": "2026-10-09T16:47:56.000Z",
      "distro": "resolute",
      "commit": "2a5ef57a6d6c66691f2aaa43de174073bed9a90e",
      "fileid": "https://r2.ropensci.org/12efc287a959719d64dc3b721df06cc3e9f402020e4c87dba5e8cdbb732e8e78",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/immcantation/actions/runs/37960805525"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.2.0.999",
      "date": "2026-10-09T16:47:59.000Z",
      "distro": "resolute",
      "commit": "2a5ef57a6d6c66691f2aaa43de174073bed9a90e",
      "fileid": "https://r2.ropensci.org/283e944822e72bd5e94562172b9f1b443e5b625f7a5825dff7d84cfc7344a513",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/immcantation/actions/runs/37960805525"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.2.0.999",
      "date": "2026-10-09T17:17:17.000Z",
      "commit": "2a5ef57a6d6c66691f2aaa43de174073bed9a90e",
      "fileid": "https://r2.ropensci.org/83c83f8ee91b13b7d021611ede8918403a6955966a38788e0e6667cd8279b6c0",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/immcantation/actions/runs/37960805525"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.2.0.999",
      "date": "2026-10-09T17:12:29.000Z",
      "commit": "2a5ef57a6d6c66691f2aaa43de174073bed9a90e",
      "fileid": "https://r2.ropensci.org/b9a4198cce7198590705821a3a1b7b5ab862f15b66c671c3f2bb42e270cb263c",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/immcantation/actions/runs/37960805525"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.2.0.999",
      "date": "2026-10-09T16:48:04.000Z",
      "commit": "2a5ef57a6d6c66691f2aaa43de174073bed9a90e",
      "fileid": "https://r2.ropensci.org/00579c1e26b578a25e213d4fcd2daa37ccf821ac2ce7641613afd34c565a1f63",
      "status": "success",
      "buildurl": "https://github.com/r-universe/immcantation/actions/runs/37960805525"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.2.0.999",
      "date": "2026-10-09T16:46:49.000Z",
      "commit": "2a5ef57a6d6c66691f2aaa43de174073bed9a90e",
      "fileid": "https://r2.ropensci.org/9fa18f957598eb0524d4ee0ca7016fcd5356bbe248a74e5cdd0344d8dede8ca8",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/immcantation/actions/runs/37960805525"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.2.0.999",
      "date": "2026-10-09T16:46:49.000Z",
      "commit": "2a5ef57a6d6c66691f2aaa43de174073bed9a90e",
      "fileid": "https://r2.ropensci.org/66d8f15ba412c8b7a9f88c4d205f20c5d96da85e19d0e4a1114242c1d1381608",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/immcantation/actions/runs/37960805525"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.2.0.999",
      "date": "2026-10-09T16:46:39.000Z",
      "commit": "2a5ef57a6d6c66691f2aaa43de174073bed9a90e",
      "fileid": "https://r2.ropensci.org/d6dd0411ad65adb041306a9b2eca267c2193a643978ab420192cbc483da3aed2",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/immcantation/actions/runs/37960805525"
    }
  ]
}