{
  "_id": "6ad5c098d423e4b0c576c3cb",
  "Package": "TCRconvertR",
  "Type": "Package",
  "Title": "Convert TCR Gene Names",
  "Description": "Convert T Cell Receptor (TCR) gene names between the 10X\nGenomics, Adaptive Biotechnologies, and ImMunoGeneTics (IMGT)\nnomenclatures.",
  "Version": "1.0",
  "Authors@R": "c(person(\"Emma\", \"Bishop\", role = c(\"aut\", \"cre\", \"cph\"),\nemail = \"emmab5@uw.edu\", comment = c(ORCID = \"0000-0003-4484-3336\")))",
  "License": "MIT + file LICENSE",
  "URL": "https://github.com/seshadrilab/tcrconvertr,\nhttps://seshadrilab.github.io/tcrconvertr/",
  "BugReports": "https://github.com/seshadrilab/tcrconvertr/issues",
  "Roxygen": "list(markdown = TRUE, roclets = c(\"collate\", \"namespace\",\n\"rd\", \"roxyglobals::global_roclet\"))",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.3.3",
  "Config/testthat/edition": "3",
  "Config/roxyglobals/filename": "globals.R",
  "Config/roxyglobals/unique": "FALSE",
  "VignetteBuilder": "knitr",
  "Repository": "https://seshadrilab.r-universe.dev",
  "Date/Publication": "2026-05-15 04:21:52 UTC",
  "RemoteUrl": "https://github.com/seshadrilab/tcrconvertr",
  "RemoteRef": "HEAD",
  "RemoteSha": "3465ddbff2fab7bd648b895d39a597f6a31f7fca",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-19 06:53:02 UTC",
    "User": "root"
  },
  "Author": "Emma Bishop [aut, cre, cph] (ORCID:\n<https://orcid.org/0000-0003-4484-3336>)",
  "Maintainer": "Emma Bishop <emmab5@uw.edu>",
  "_user": "seshadrilab",
  "_type": "src",
  "_file": "TCRconvertR_1.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/5c1b0148bdae145c3c1cbaef76a0e8cf7edd1d4e7cd49cbfcacf05780725b65a",
  "_filesize": 163338,
  "_sha256": "5c1b0148bdae145c3c1cbaef76a0e8cf7edd1d4e7cd49cbfcacf05780725b65a",
  "_expires": "2027-01-27T07:02:46.000Z",
  "_created": "2026-10-19T06:53:02.000Z",
  "_published": "2026-10-19T07:02:48.657Z",
  "_buildurl": "https://github.com/r-universe/seshadrilab/actions/runs/39212192186",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_jobs": [
    {
      "job": 117928894204,
      "time": 122,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "12167839652"
    },
    {
      "job": 117928894268,
      "time": 93,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12168013385"
    },
    {
      "job": 117928894084,
      "time": 192,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "12168178193"
    },
    {
      "job": 117928894143,
      "time": 154,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12168318433"
    },
    {
      "job": 117927952308,
      "time": 183,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12167988238"
    },
    {
      "job": 117928894161,
      "time": 87,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "12168441640"
    },
    {
      "job": 117928894216,
      "time": 63,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "12167703375"
    },
    {
      "job": 117928894162,
      "time": 64,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "12167683441"
    },
    {
      "job": 117928894065,
      "time": 63,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12168446375"
    }
  ],
  "_upstream": "https://github.com/seshadrilab/tcrconvertr",
  "_commit": {
    "id": "3465ddbff2fab7bd648b895d39a597f6a31f7fca",
    "author": "Emma Bishop <46635347+emjbishop@users.noreply.github.com>",
    "committer": "GitHub <noreply@github.com>",
    "message": "Merge pull request #31 from seshadrilab/fix-empty-warning\n\nStrip NAs from bad_genes_all before checking length",
    "time": 1778818912
  },
  "_maintainer": {
    "name": "Emma Bishop",
    "email": "emmab5@uw.edu",
    "login": "emjbishop",
    "linkedin": "in/emma-bishop-emjbishop",
    "orcid": "0000-0003-4484-3336",
    "description": "Bioinformatics Data Scientist @ Fred Hutch",
    "uuid": 46635347
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "rappdirs",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "roxyglobals",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    },
    {
      "package": "mockery",
      "role": "Suggests"
    }
  ],
  "_owner": "seshadrilab",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-51",
      "n": 1
    },
    {
      "week": "2025-52",
      "n": 1
    },
    {
      "week": "2026-20",
      "n": 1
    }
  ],
  "_tags": [],
  "_stars": 6,
  "_contributors": [
    {
      "user": "emjbishop",
      "count": 144,
      "uuid": 46635347
    },
    {
      "user": "mxsmi",
      "count": 7,
      "uuid": 45386017
    }
  ],
  "_userbio": {
    "uuid": 26777072,
    "type": "organization",
    "name": "Seshadri Lab",
    "followers": 2
  },
  "_downloads": {
    "count": 297,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/TCRconvertR"
  },
  "_devurl": "https://github.com/seshadrilab/tcrconvertr",
  "_pkgdown": "https://seshadrilab.github.io/tcrconvertr/",
  "_searchresults": 5,
  "_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/TCRconvertR.html",
    "LICENSE"
  ],
  "_homeurl": "https://github.com/seshadrilab/tcrconvertr",
  "_realowner": "seshadrilab",
  "_cranurl": true,
  "_releases": [
    {
      "version": "1.0",
      "date": "2025-04-17"
    }
  ],
  "_exports": [
    "add_dash_one",
    "build_lookup_from_fastas",
    "choose_lookup",
    "convert_gene",
    "extract_imgt_genes",
    "get_example_path",
    "pad_single_digit",
    "parse_imgt_fasta",
    "parse_mixcr_csv",
    "save_lookup",
    "which_frm_cols"
  ],
  "_help": [
    {
      "page": "build_lookup_from_fastas",
      "title": "Create lookup tables",
      "topics": [
        "build_lookup_from_fastas"
      ]
    },
    {
      "page": "convert_gene",
      "title": "Convert gene names",
      "topics": [
        "convert_gene"
      ]
    },
    {
      "page": "get_example_path",
      "title": "Get full path to an example file or directory",
      "topics": [
        "get_example_path"
      ]
    }
  ],
  "_readme": "https://github.com/seshadrilab/tcrconvertr/raw/HEAD/README.md",
  "_rundeps": [
    "rappdirs"
  ],
  "_vignettes": [
    {
      "source": "TCRconvertR.Rmd",
      "filename": "TCRconvertR.html",
      "title": "Get started",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Installation",
        "Basic usage",
        "1. Load TCRs into a data frame",
        "2. Convert",
        "AIRR data",
        "Custom column names",
        "Rhesus or mouse data"
      ],
      "created": "2025-03-07 02:43:38",
      "modified": "2025-04-23 21:24:51",
      "commits": 4
    },
    {
      "source": "custom-species.Rmd",
      "filename": "custom-species.html",
      "title": "Using a custom species",
      "engine": "knitr::rmarkdown",
      "headings": [
        "1. Create a folder of IMGT FASTA files",
        "2. Run build_lookup_from_fastas()"
      ],
      "created": "2025-03-07 02:43:38",
      "modified": "2025-03-07 02:43:38",
      "commits": 1
    }
  ],
  "_score": 5.2552725051033065,
  "_indexed": true,
  "_nocasepkg": "tcrconvertr",
  "_universes": [
    "seshadrilab",
    "emjbishop"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.0",
      "date": "2026-10-19T06:55:06.000Z",
      "distro": "resolute",
      "commit": "3465ddbff2fab7bd648b895d39a597f6a31f7fca",
      "fileid": "https://r2.ropensci.org/47f13c449194c1854122457822a5817ba1593470c69636d980741379746e9578",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/seshadrilab/actions/runs/39212192186"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.0",
      "date": "2026-10-19T06:54:40.000Z",
      "distro": "resolute",
      "commit": "3465ddbff2fab7bd648b895d39a597f6a31f7fca",
      "fileid": "https://r2.ropensci.org/1f2fc92d40f5e2557632670fb6eddfa323401b9d9181b318de2cbdc6541ebc0a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/seshadrilab/actions/runs/39212192186"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.0",
      "date": "2026-10-19T06:57:50.000Z",
      "commit": "3465ddbff2fab7bd648b895d39a597f6a31f7fca",
      "fileid": "https://r2.ropensci.org/c0be61a12c44e7a5729e6d370f1349fbc3fd4a6d3c5e4f11a98419ff4ee98fec",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/seshadrilab/actions/runs/39212192186"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.0",
      "date": "2026-10-19T07:01:49.000Z",
      "commit": "3465ddbff2fab7bd648b895d39a597f6a31f7fca",
      "fileid": "https://r2.ropensci.org/fb9c22ec51d3bd24df6ef61fc331534dd5879dd701f217edf3ca59b5c3c4d496",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/seshadrilab/actions/runs/39212192186"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.0",
      "date": "2026-10-19T06:54:42.000Z",
      "commit": "3465ddbff2fab7bd648b895d39a597f6a31f7fca",
      "fileid": "https://r2.ropensci.org/37cea9fe718c3cdc35fac28de3b9bec0af75f65cbeb3aa723120c64d4e606f5a",
      "status": "success",
      "buildurl": "https://github.com/r-universe/seshadrilab/actions/runs/39212192186"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.0",
      "date": "2026-10-19T06:54:01.000Z",
      "commit": "3465ddbff2fab7bd648b895d39a597f6a31f7fca",
      "fileid": "https://r2.ropensci.org/585a2724f3742ccf9a23095dbb6aef9b3ca3052cd204f4f2d2c945a56f304ee7",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/seshadrilab/actions/runs/39212192186"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.0",
      "date": "2026-10-19T06:54:05.000Z",
      "commit": "3465ddbff2fab7bd648b895d39a597f6a31f7fca",
      "fileid": "https://r2.ropensci.org/f71d158875fa2e87858098af63b5e11e72d9d3af210057aa11ee961965c94fcc",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/seshadrilab/actions/runs/39212192186"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.0",
      "date": "2026-10-19T06:54:03.000Z",
      "commit": "3465ddbff2fab7bd648b895d39a597f6a31f7fca",
      "fileid": "https://r2.ropensci.org/c1800631550d4ce0192e23b2ab5287da22c6e295fb4df1cf6c585fb8a467cba3",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/seshadrilab/actions/runs/39212192186"
    }
  ]
}