{
  "_id": "6ab2469c3d719c1f8408b2dd",
  "Type": "Package",
  "Package": "immunogenetr",
  "Title": "A Comprehensive Toolkit for Clinical HLA Informatics",
  "Version": "1.5.0",
  "Authors@R": "c(\nperson(\"Nicholas\", \"Brown\", , \"nicholas.brown@pennmedicine.upenn.edu\", role = c(\"cre\", \"aut\"),\ncomment = c(ORCID = \"0000-0002-0046-2315\")),\nperson(\"Busra\", \"Coskun\", , \"bcoskun@sas.upenn.edu\", role = \"aut\",\ncomment = c(ORCID = \"0009-0008-6828-3453\"))\n)",
  "Maintainer": "Nicholas Brown <nicholas.brown@pennmedicine.upenn.edu>",
  "Description": "A comprehensive toolkit for clinical Human Leukocyte\nAntigen (HLA) informatics, built on 'tidyverse'\n<https://tidyverse.tidyverse.org/> principles and making use of\nGenotype List String (GL String, Mack et al. (2023)\n<doi:10.1111/tan.15126>) for storing and computing HLA genotype\ndata.  Specific functionalities include: coercion of HLA data\nin tabular format to and from GL String; calculation of\nmatching and mismatching in all directions, with multiple\noutput formats; automatic formatting of HLA data for searching\nwithin a GL String; truncation of molecular HLA data to a\nspecific number of fields; and reading HLA genotypes in HML\nfiles and extracting the GL String. This library is intended\nfor research use. Any application making use of this package in\na clinical setting will need to be independently validated\naccording to local regulations.",
  "License": "GPL (>= 3)",
  "URL": "https://immunogenetr.org,\nhttps://github.com/k96nb01/immunogenetr_package,\nhttps://doi.org/10.1016/j.humimm.2025.111619",
  "BugReports": "https://github.com/k96nb01/immunogenetr_package/issues",
  "VignetteBuilder": "knitr",
  "Config/testthat/edition": "3",
  "Encoding": "UTF-8",
  "Language": "en-US",
  "LazyData": "true",
  "Config/roxygen2/version": "8.1.0",
  "Config/pak/sysreqs": "libicu-dev libxml2-dev",
  "Repository": "https://k96nb01.r-universe.dev",
  "Date/Publication": "2026-08-23 19:58:29 UTC",
  "RemoteUrl": "https://github.com/k96nb01/immunogenetr_package",
  "RemoteRef": "HEAD",
  "RemoteSha": "2b8c52ccad1155b16e79a010f4343f03979461ff",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-09-22 09:09:22 UTC",
    "User": "root"
  },
  "Author": "Nicholas Brown [cre, aut] (ORCID:\n<https://orcid.org/0000-0002-0046-2315>),\nBusra Coskun [aut] (ORCID: <https://orcid.org/0009-0008-6828-3453>)",
  "_user": "k96nb01",
  "_type": "src",
  "_file": "immunogenetr_1.5.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/e06f00ccc0f34e19682d98a6a46763385c0e7d26a5308ccc248a92dc4e9ef5ed",
  "_filesize": 698787,
  "_sha256": "e06f00ccc0f34e19682d98a6a46763385c0e7d26a5308ccc248a92dc4e9ef5ed",
  "_expires": "2026-12-31T09:12:58.000Z",
  "_created": "2026-09-22T09:09:22.000Z",
  "_published": "2026-09-22T09:13:00.512Z",
  "_jobs": [
    {
      "job": 106684102301,
      "time": 148,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
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  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/k96nb01/actions/runs/35708371008",
  "_status": "success",
  "_upstream": "https://github.com/k96nb01/immunogenetr_package",
  "_commit": {
    "id": "2b8c52ccad1155b16e79a010f4343f03979461ff",
    "author": "Nick Brown <83467161+k96nb01@users.noreply.github.com>",
    "committer": "GitHub <noreply@github.com>",
    "message": "CI: add job timeouts to prevent 6-hour hung runs (#50)\n\nOn 2026-08-19 six jobs stalled in r-lib/actions/setup-r@v2 and ran to\nGitHub's 6-hour default job cap before being cancelled, consuming 2,242\nof the month's 2,336 Linux minutes. The repo is public so nothing was\nbilled, but the jobs blocked PR checks for six hours.\n\nAdd explicit timeout-minutes to every job:\n  R-CMD-check    75  (per matrix leg)\n  pkgdown        60\n  test-coverage  60\n  rhub setup     15\n  rhub checks    90\n\nSized above the slowest observed *successful* job, not the typical one:\non that same degraded day the ubuntu-latest (release) leg spent 43.5 min\nin setup-r and still passed at 44.8 min total, so a tighter cap would\nfail healthy runs.\n\nBecause fail-fast is false, a systemic stall times out every matrix leg\nindependently, so worst case per R-CMD-check run drops from 5 x 360 =\n1800 min to 5 x 75 = 375 min.\n\nAlso document rhub.yaml's local modifications, which rhub::rhub_setup()\nwould otherwise silently overwrite.\n\nCo-authored-by: Claude Opus 5 (1M context) <noreply@anthropic.com>",
    "time": 1787515109
  },
  "_maintainer": {
    "name": "Nicholas Brown",
    "email": "nicholas.brown@pennmedicine.upenn.edu",
    "login": "k96nb01",
    "orcid": "0000-0002-0046-2315",
    "description": "HLA lab director and Associate Professor at Penn. ",
    "uuid": 83467161
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
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      "role": "Depends"
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      "version": ">= 3.0.0",
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      "role": "Suggests"
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  "_owner": "k96nb01",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
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      "week": "2025-43",
      "n": 2
    },
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      "week": "2026-15",
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  "_tags": [
    {
      "name": "v1.1.0",
      "date": "2026-04-06"
    },
    {
      "name": "v1.2.0",
      "date": "2026-04-10"
    },
    {
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      "date": "2026-05-26"
    },
    {
      "name": "v1.4.0",
      "date": "2026-07-06"
    },
    {
      "name": "CRAN",
      "date": "2026-08-19"
    },
    {
      "name": "v1.5.0",
      "date": "2026-08-19"
    }
  ],
  "_topics": [
    "hla",
    "hla-typing",
    "informatics",
    "tidyverse"
  ],
  "_stars": 6,
  "_contributors": [
    {
      "user": "k96nb01",
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      "uuid": 83467161
    },
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  "_userbio": {
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    "type": "user",
    "name": "Nick Brown",
    "followers": 22,
    "description": "HLA lab director and Associate Professor at Penn. "
  },
  "_downloads": {
    "count": 345,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/immunogenetr"
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  "_devurl": "https://github.com/k96nb01/immunogenetr_package",
  "_pkgdown": "https://immunogenetr.org",
  "_searchresults": 25,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/immunogenetr.html",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md"
  ],
  "_homeurl": "https://github.com/k96nb01/immunogenetr_package",
  "_realowner": "k96nb01",
  "_cranurl": true,
  "_releases": [
    {
      "version": "0.1.0",
      "date": "2025-03-24"
    },
    {
      "version": "0.2.0",
      "date": "2025-06-06"
    },
    {
      "version": "0.3.0",
      "date": "2025-06-18"
    },
    {
      "version": "0.3.1",
      "date": "2025-06-25"
    },
    {
      "version": "1.0.0",
      "date": "2025-08-19"
    },
    {
      "version": "1.0.1",
      "date": "2025-10-23"
    },
    {
      "version": "1.1.0",
      "date": "2026-04-07"
    },
    {
      "version": "1.2.0",
      "date": "2026-04-14"
    },
    {
      "version": "1.3.0",
      "date": "2026-05-26"
    },
    {
      "version": "1.4.0",
      "date": "2026-07-06"
    },
    {
      "version": "1.5.0",
      "date": "2026-08-19"
    }
  ],
  "_exports": [
    "ambiguity_table_to_GLstring",
    "GLstring_drop_non_expressed",
    "GLstring_expand_longer",
    "GLstring_gene_copies_combine",
    "GLstring_genes",
    "GLstring_genes_expanded",
    "GLstring_genotype_ambiguity",
    "GLstring_regex",
    "GLstring_to_ambiguity_table",
    "HLA_column_repair",
    "HLA_columns_to_GLstring",
    "HLA_match_number",
    "HLA_match_summary_HCT",
    "HLA_mismatch_alleles",
    "HLA_mismatch_base",
    "HLA_mismatch_logical",
    "HLA_mismatch_number",
    "HLA_mismatched_alleles",
    "HLA_prefix_add",
    "HLA_prefix_remove",
    "HLA_truncate",
    "HLA_validate",
    "read_HML"
  ],
  "_datasets": [
    {
      "name": "Haplotype_frequencies",
      "title": "Ten HLA-A~C~B~DRB3/4/5~DRB1~DQA1~DQB1~DPA1~DPB1 haplotypes and their frequencies in the global population.",
      "object": "Haplotype_frequencies",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "HLA-A",
        "HLA-C",
        "HLA-B",
        "HLA-DRB345",
        "HLA-DRB1",
        "HLA-DQA1",
        "HLA-DQB1",
        "HLA-DPA1",
        "HLA-DPB1",
        "Global_Fq",
        "Global_n",
        "Global_rank"
      ],
      "rows": 10,
      "table": true,
      "tojson": true
    },
    {
      "name": "HLA_dictionary",
      "title": "Data on HLA alleles in the 2008 HLA dictionary",
      "object": "HLA_dictionary",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "IPD.Accession",
        "HLA.Allele",
        "WHO.Assigned.Type"
      ],
      "rows": 100,
      "table": true,
      "tojson": true
    },
    {
      "name": "HLA_typing_1",
      "title": "Synthetic HLA typing data for 10 individuals for the HLA-A, B, C, DRB1, DRB3/4/5, DQB1, DQA1, DPB1 and DPA1 loci.",
      "object": "HLA_typing_1",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "patient",
        "A1",
        "A2",
        "C1",
        "C2",
        "B1",
        "B2",
        "DRB345_1",
        "DRB345_2",
        "DRB1_1",
        "DRB1_2",
        "DQA1_1",
        "DQA1_2",
        "DQB1_1",
        "DQB1_2",
        "DPA1_1",
        "DPA1_2",
        "DPB1_1",
        "DPB1_2"
      ],
      "rows": 10,
      "table": true,
      "tojson": true
    },
    {
      "name": "HLA_typing_LIS",
      "title": "Synthetic HLA typing data for 10 individuals for the HLA-A, B, C, DRB1, DRB3, DRB4, DRB5, DQB1, DQA1, DPB1 and DPA1 loci. Data formatted to resemble a HistoTrac table.",
      "object": "HLA_typing_LIS",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "patient",
        "mA1Cd.recipient",
        "mA2Cd.recipient",
        "mB1Cd.recipient",
        "mB2Cd.recipient",
        "mC1Cd.recipient",
        "mC2Cd.recipient",
        "mDRB11Cd.recipient",
        "mDRB12Cd.recipient",
        "mDRB31cd.recipient",
        "mDRB32cd.recipient",
        "mDRB41cd.recipient",
        "mDRB42cd.recipient",
        "mDRB51cd.recipient",
        "mDRB52cd.recipient",
        "mDQA11Cd.recipient",
        "mDQA12Cd.recipient",
        "mDQB11cd.recipient",
        "mDQB12cd.recipient",
        "mDPA11Cd.recipient",
        "mDPA12Cd.recipient",
        "mDPB11cd.recipient",
        "mDPB12cd.recipient"
      ],
      "rows": 10,
      "table": true,
      "tojson": true
    },
    {
      "name": "HLA_typing_synthetic_LIS",
      "title": "Synthetic clinical-laboratory HLA typing table (HistoTrac \"Patient\" layout).",
      "object": "HLA_typing_synthetic_LIS",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "PatientId",
        "UNOSId",
        "HospitalID",
        "PhysicianID",
        "firstnm",
        "lastnm",
        "DOB",
        "categoryCd",
        "RaceCd",
        "GenderCd",
        "ABOCd",
        "A1Cd",
        "A2Cd",
        "B1Cd",
        "B2Cd",
        "BW1Cd",
        "Bw2Cd",
        "Cw1Cd",
        "Cw2Cd",
        "DR1Cd",
        "DR2Cd",
        "drw1cd",
        "drw2cd",
        "dq1cd",
        "dq2cd",
        "PatientTypeCd",
        "mA1Cd",
        "mA2Cd",
        "mB1Cd",
        "mB2Cd",
        "mC1Cd",
        "mC2Cd",
        "mDRB11Cd",
        "mDRB12Cd",
        "mDRB31cd",
        "mDRB32cd",
        "mDRB41cd",
        "mDRB42cd",
        "mDRB51cd",
        "mDRB52cd",
        "mDQA11Cd",
        "mDQA12Cd",
        "mDQB11cd",
        "mDQB12cd",
        "mDPA11Cd",
        "mDPA12Cd",
        "mDPB11cd",
        "mDPB12cd",
        "UNOSCPRAAmt",
        "StatusCd",
        "UnacceptAntigenTxt",
        "ModerateRiskAntibodyTxt",
        "UNOSUnacceptAntigenTxt"
      ],
      "rows": 63,
      "table": true,
      "tojson": true
    },
    {
      "name": "mismatch_table_2010",
      "title": "Consensus mismatch numbers for every possible allele combination at a single locus, from the 2010 publication.",
      "object": "mismatch_table_2010",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "patient",
        "donor",
        "#GvH",
        "#HvG",
        "#Total",
        "#Max"
      ],
      "rows": 26,
      "table": true,
      "tojson": true
    },
    {
      "name": "mismatch_table_2016",
      "title": "Consensus mismatch numbers for every possible allele combination at a single locus, from the 2016 publication.",
      "object": "mismatch_table_2016",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "Patient",
        "Donor",
        "#GvH",
        "#HvG",
        "#Max"
      ],
      "rows": 26,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "ambiguity_table_to_GLstring",
      "title": "ambiguity_table_to_GLstring",
      "topics": [
        "ambiguity_table_to_GLstring"
      ]
    },
    {
      "page": "GLstring_drop_non_expressed",
      "title": "GLstring_drop_non_expressed",
      "topics": [
        "GLstring_drop_non_expressed"
      ]
    },
    {
      "page": "GLstring_expand_longer",
      "title": "GLstring_expand_longer",
      "topics": [
        "GLstring_expand_longer"
      ]
    },
    {
      "page": "GLstring_gene_copies_combine",
      "title": "GLstring_gene_copies_combine",
      "topics": [
        "GLstring_gene_copies_combine"
      ]
    },
    {
      "page": "GLstring_genes",
      "title": "GLstring_genes",
      "topics": [
        "GLstring_genes"
      ]
    },
    {
      "page": "GLstring_genes_expanded",
      "title": "GLstring_genes_expanded",
      "topics": [
        "GLstring_genes_expanded"
      ]
    },
    {
      "page": "GLstring_genotype_ambiguity",
      "title": "GLstring_genotype_ambiguity",
      "topics": [
        "GLstring_genotype_ambiguity"
      ]
    },
    {
      "page": "GLstring_regex",
      "title": "GLstring_regex",
      "topics": [
        "GLstring_regex"
      ]
    },
    {
      "page": "GLstring_to_ambiguity_table",
      "title": "GLstring_to_ambiguity_table",
      "topics": [
        "GLstring_to_ambiguity_table"
      ]
    },
    {
      "page": "Haplotype_frequencies",
      "title": "Ten HLA-A~C~B~DRB3/4/5~DRB1~DQA1~DQB1~DPA1~DPB1 haplotypes and their frequencies in the global population.",
      "topics": [
        "Haplotype_frequencies"
      ]
    },
    {
      "page": "HLA_column_repair",
      "title": "HLA_column_repair",
      "topics": [
        "HLA_column_repair"
      ]
    },
    {
      "page": "HLA_columns_to_GLstring",
      "title": "HLA_columns_to_GLstring",
      "topics": [
        "HLA_columns_to_GLstring"
      ]
    },
    {
      "page": "HLA_dictionary",
      "title": "Data on HLA alleles in the 2008 HLA dictionary",
      "topics": [
        "HLA_dictionary"
      ]
    },
    {
      "page": "HLA_match_number",
      "title": "HLA_match_number",
      "topics": [
        "HLA_match_number"
      ]
    },
    {
      "page": "HLA_match_summary_HCT",
      "title": "HLA_match_summary_HCT",
      "topics": [
        "HLA_match_summary_HCT"
      ]
    },
    {
      "page": "HLA_mismatch_alleles",
      "title": "HLA_mismatch_alleles",
      "topics": [
        "HLA_mismatch_alleles"
      ]
    },
    {
      "page": "HLA_mismatch_base",
      "title": "HLA_mismatch_base",
      "topics": [
        "HLA_mismatch_base"
      ]
    },
    {
      "page": "HLA_mismatch_logical",
      "title": "HLA_mismatch_logical",
      "topics": [
        "HLA_mismatch_logical"
      ]
    },
    {
      "page": "HLA_mismatch_number",
      "title": "HLA_mismatch_number",
      "topics": [
        "HLA_mismatch_number"
      ]
    },
    {
      "page": "HLA_mismatched_alleles",
      "title": "HLA_mismatched_alleles",
      "topics": [
        "HLA_mismatched_alleles"
      ]
    },
    {
      "page": "HLA_prefix_add",
      "title": "HLA_prefix_add",
      "topics": [
        "HLA_prefix_add"
      ]
    },
    {
      "page": "HLA_prefix_remove",
      "title": "HLA_prefix_remove",
      "topics": [
        "HLA_prefix_remove"
      ]
    },
    {
      "page": "HLA_truncate",
      "title": "HLA_truncate",
      "topics": [
        "HLA_truncate"
      ]
    },
    {
      "page": "HLA_typing_1",
      "title": "Synthetic HLA typing data for 10 individuals for the HLA-A, B, C, DRB1, DRB3/4/5, DQB1, DQA1, DPB1 and DPA1 loci.",
      "topics": [
        "HLA_typing_1"
      ]
    },
    {
      "page": "HLA_typing_LIS",
      "title": "Synthetic HLA typing data for 10 individuals for the HLA-A, B, C, DRB1, DRB3, DRB4, DRB5, DQB1, DQA1, DPB1 and DPA1 loci. Data formatted to resemble a HistoTrac table.",
      "topics": [
        "HLA_typing_LIS"
      ]
    },
    {
      "page": "HLA_typing_synthetic_LIS",
      "title": "Synthetic clinical-laboratory HLA typing table (HistoTrac \"Patient\" layout).",
      "topics": [
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    },
    {
      "page": "HLA_validate",
      "title": "HLA_validate",
      "topics": [
        "HLA_validate"
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    },
    {
      "page": "mismatch_table_2010",
      "title": "Consensus mismatch numbers for every possible allele combination at a single locus, from the 2010 publication.",
      "topics": [
        "mismatch_table_2010"
      ]
    },
    {
      "page": "mismatch_table_2016",
      "title": "Consensus mismatch numbers for every possible allele combination at a single locus, from the 2016 publication.",
      "topics": [
        "mismatch_table_2016"
      ]
    },
    {
      "page": "read_HML",
      "title": "read_HML",
      "topics": [
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  ],
  "_readme": "https://github.com/k96nb01/immunogenetr_package/raw/HEAD/README.md",
  "_rundeps": [
    "cli",
    "cpp11",
    "dplyr",
    "generics",
    "glue",
    "lifecycle",
    "magrittr",
    "pillar",
    "pkgconfig",
    "purrr",
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  "_vignettes": [
    {
      "source": "immunogenetr.Rmd",
      "filename": "immunogenetr.html",
      "title": "Getting Started with immunogenetr",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "Setup",
        "Converting tabular HLA data to GL Strings",
        "Splitting GL Strings into loci",
        "Calculating HLA mismatches",
        "Is there a mismatch? (HLA_mismatch_logical)",
        "How many mismatches? (HLA_mismatch_number)",
        "Which alleles are mismatched? (HLA_mismatched_alleles)",
        "Match count (HLA_match_number)",
        "HLA match summaries for transplantation",
        "Finding the best donor",
        "Working with HLA allele names",
        "Truncation",
        "Prefix management",
        "Regex for GL String searching",
        "Removing non-expressed alleles",
        "Column name repair",
        "Reading HML files",
        "Disclaimer"
      ],
      "created": "2026-04-06 20:19:11",
      "modified": "2026-08-16 19:58:22",
      "commits": 4
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  "_indexed": true,
  "_nocasepkg": "immunogenetr",
  "_universes": [
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