{ "_id": "6a23598d530b9bc726bd5db7", "Type": "Package", "Package": "immunogenetr", "Title": "A Comprehensive Toolkit for Clinical HLA Informatics", "Version": "1.3.0", "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 ", "Description": "A comprehensive toolkit for clinical Human Leukocyte\nAntigen (HLA) informatics, built on 'tidyverse'\n principles and making use of\ngenotype list string (GL string, Mack et al. (2023)\n) 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": "8.0.0", "Config/pak/sysreqs": "libicu-dev libxml2-dev", "Repository": "https://k96nb01.r-universe.dev", "Date/Publication": "2026-06-05 22:24:37 UTC", "RemoteUrl": "https://github.com/k96nb01/immunogenetr_package", "RemoteRef": "HEAD", "RemoteSha": "4b2364fa5f8c2871acddf90eb8104d5fb6d26ee8", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-05 23:15:59 UTC", "User": "root" }, "Author": "Nicholas Brown [cre, aut] (ORCID:\n),\nBusra Coskun [aut] (ORCID: )", "MD5sum": "629287057539770c3f9de7e1bbb73657", "_user": "k96nb01", "_type": "src", "_file": "immunogenetr_1.3.0.tar.gz", "_fileid": "8c2372d89d2414f3b70601389a3435e8ec679d1fa67531b15ecf5fdadf515f90", "_filesize": 646522, "_sha256": "8c2372d89d2414f3b70601389a3435e8ec679d1fa67531b15ecf5fdadf515f90", "_created": "2026-06-05T23:15:59.000Z", "_published": "2026-06-05T23:19:41.160Z", "_distro": "noble", "_jobs": [ { "job": 79829261481, "time": 137, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7448653884" }, { "job": 79829261450, "time": 143, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7448655087" }, { "job": 79829261489, "time": 190, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7448662300" }, { "job": 79829261463, "time": 128, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7448652311" }, { "job": 79829005549, "time": 159, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7448629625" }, { "job": 79829261422, "time": 123, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7448651513" }, { "job": 79829261461, "time": 90, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7448646016" }, { "job": 79829261466, "time": 93, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7448646468" }, { "job": 79829261460, "time": 100, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7448647812" } ], "_buildurl": "https://github.com/r-universe/k96nb01/actions/runs/27044983752", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/k96nb01/immunogenetr_package", "_commit": { "id": "4b2364fa5f8c2871acddf90eb8104d5fb6d26ee8", "author": "Nick Brown <83467161+k96nb01@users.noreply.github.com>", "committer": "GitHub ", "message": "Docs: add CRAN version + downloads badges, update SOP (#39)\n\n* SOP: rewrite Phase 4, add Phase 5.2, fix dev branch reset guidance\n\nTwelve fixes based on issues that surfaced during the 1.3.0 release:\n\nStructural:\n- Add Phase 4 ordering callout explaining the 4.1 -> 4.2 -> 4.3/4.4 ->\n 3.4 -> 4.5 interleave. Branch protection on master forces the version\n bump and checks to happen on dev before merging.\n- Add Phase 5.2 \"Begin the next release cycle\" closing the loop back to\n Phase 1. The mechanics were in 1.3 but there was no pointer from the\n end of Phase 5.\n- Fix 1.3: squash-merge makes dev/master diverge, so `merge --ff-only`\n fails. Replace with `reset --hard master` + force-with-lease push.\n\nPhase 4.3:\n- Drop the standalone `devtools::check()` line; `check(remote = TRUE,\n manual = TRUE)` is the strict superset.\n- Add `devtools::check_win_devel()` as an explicit step. Windows-R-release\n locally is not Windows-R-devel on win-builder.\n- Replace local `rhub::rhub_check()` guidance with `rhub.yaml`\n workflow_dispatch. rhub v2 runs on GHA runners anyway; local install\n is just a remote queue. Recommend `donttest`, `nosuggests`, `gcc16`\n as the platforms that add coverage beyond the GHA matrix.\n- Add TinyTeX troubleshooting subsection covering the three tripwires\n hit during 1.3.0 prep: stale TeX Live year, missing font packages\n (note that urw-base35 is NOT on Yihui's mirror), and missing\n `makeindex`. Document the wipe-Rcheck step before re-running.\n- Warn that devtools::check()'s bottom summary box silently drops\n ERRORs. Trust the mid-output `Status: N ERROR, ...` line.\n\nPhase 4.4:\n- Make cran-comments.md template platform-agnostic.\n- Add subsection documenting the R-hub `nosuggests` + rmarkdown\n vignette interaction (ERROR on R-hub, NOTE on CRAN with\n `_R_CHECK_FORCE_SUGGESTS_=false`) with copy-pasteable disclosure\n template.\n\nPhase 4.5:\n- Expand to explain: `submit_cran()` doesn't actually submit — CRAN\n emails a confirmation link that the mainta", "time": 1780698277 }, "_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 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "cli", "version": ">= 3.0.0", "role": "Imports" }, { "package": "dplyr", "version": ">= 1.1.1", "role": "Imports" }, { "package": "purrr", "version": ">= 1.0.2", "role": "Imports" }, { "package": "rlang", "version": ">= 1.1.2", "role": "Imports" }, { "package": "stringi", "version": ">= 1.7.0", "role": "Imports" }, { "package": "stringr", "version": ">= 1.5.0", "role": "Imports" }, { "package": "tibble", "version": ">= 3.1.3", "role": "Imports" }, { "package": "tidyr", "version": ">= 1.3.0", "role": "Imports" }, { "package": "tidyselect", "version": ">= 1.2.0", "role": "Imports" }, { "package": "xml2", "version": ">= 1.3.6", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "k96nb01", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-26", "n": 2 }, { "week": "2025-32", "n": 4 }, { "week": "2025-34", "n": 1 }, { "week": "2025-43", "n": 2 }, { "week": "2026-15", "n": 7 }, { "week": "2026-17", "n": 1 }, { "week": "2026-20", "n": 2 }, { "week": "2026-22", "n": 3 }, { "week": "2026-23", "n": 1 } ], "_tags": [ { "name": "v1.1.0", "date": "2026-04-06" }, { "name": "v1.2.0", "date": "2026-04-10" }, { "name": "v1.3.0", "date": "2026-05-26" } ], "_topics": [ "hla", "hla-typing", "informatics", "tidyverse" ], "_stars": 6, "_contributors": [ { "user": "k96nb01", "count": 477, "uuid": 83467161 }, { "user": "busracoskun", "count": 1, "uuid": 92342801 } ], "_userbio": { "uuid": 83467161, "type": "user", "name": "Nick Brown", "description": "HLA lab director and Associate Professor at Penn. " }, "_downloads": { "count": 542, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/immunogenetr" }, "_devurl": "https://github.com/k96nb01/immunogenetr_package", "_pkgdown": "https://immunogenetr.org", "_searchresults": 30, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/immunogenetr.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_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" } ], "_exports": [ "ambiguity_table_to_GLstring", "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": "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_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_validate", "title": "HLA_validate", "topics": [ "HLA_validate" ] }, { "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": [ "read_HML" ] } ], "_readme": "https://github.com/k96nb01/immunogenetr_package/raw/HEAD/README.md", "_rundeps": [ "cli", "cpp11", "dplyr", "generics", "glue", "lifecycle", "magrittr", "pillar", "pkgconfig", "purrr", "R6", "rlang", "stringi", "stringr", "tibble", "tidyr", "tidyselect", "utf8", "vctrs", "withr", "xml2" ], "_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", "Column name repair", "Reading HML files", "Disclaimer" ], "created": "2026-04-06 20:19:11", "modified": "2026-05-11 23:59:02", "commits": 2 } ], "_score": 5.9084850188786495, "_indexed": true, "_nocasepkg": "immunogenetr", "_universes": [ "k96nb01" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.3.0", "date": "2026-06-05T23:18:06.000Z", "distro": "noble", "commit": "4b2364fa5f8c2871acddf90eb8104d5fb6d26ee8", "fileid": "7f108991c65a500ba256de2fda6d0c6fc77d27b6dbc7e6005f06c8bb00591b53", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/k96nb01/actions/runs/27044983752" }, { "r": "4.6.0", "os": "linux", "version": "1.3.0", "date": "2026-06-05T23:18:12.000Z", "distro": "noble", "commit": "4b2364fa5f8c2871acddf90eb8104d5fb6d26ee8", "fileid": "16fc60ac5ee60c90afcbf9ecd73cfd588acbc9bb67a501ce380a9d5ddfaf2c61", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/k96nb01/actions/runs/27044983752" }, { "r": "4.5.3", "os": "mac", "version": "1.3.0", "date": "2026-06-05T23:19:01.000Z", "commit": "4b2364fa5f8c2871acddf90eb8104d5fb6d26ee8", "fileid": "5a4d04ae5153a4e99bf7d02b1856834a07dfc4e8d8179bbbdf3b6dd715018642", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/k96nb01/actions/runs/27044983752" }, { "r": "4.6.0", "os": "mac", "version": "1.3.0", "date": "2026-06-05T23:18:00.000Z", "commit": "4b2364fa5f8c2871acddf90eb8104d5fb6d26ee8", "fileid": "bf4f3f2a85d0289f9ae48d0598454932800fe65526168a34570eacaeefc058c7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/k96nb01/actions/runs/27044983752" }, { "r": "4.6.0", "os": "wasm", "version": "1.3.0", "date": "2026-06-05T23:18:16.000Z", "commit": "4b2364fa5f8c2871acddf90eb8104d5fb6d26ee8", "fileid": "61956324251c9d4e5f2f57e70afcd9c80d989e80c7abdd3bf385bb003c89fab1", "status": "success", "buildurl": "https://github.com/r-universe/k96nb01/actions/runs/27044983752" }, { "r": "4.7.0", "os": "win", "version": "1.3.0", "date": "2026-06-05T23:17:10.000Z", "commit": "4b2364fa5f8c2871acddf90eb8104d5fb6d26ee8", "fileid": "2b5055f810b479bd25d641cf9b05cf356173fde83e68f01b474330a67c599b97", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/k96nb01/actions/runs/27044983752" }, { "r": "4.5.3", "os": "win", "version": "1.3.0", "date": "2026-06-05T23:17:10.000Z", "commit": "4b2364fa5f8c2871acddf90eb8104d5fb6d26ee8", "fileid": "e789dfee1d2b1cf55e754aa1034ff8d109c41172391da98f51f459584d2da46f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/k96nb01/actions/runs/27044983752" }, { "r": "4.6.0", "os": "win", "version": "1.3.0", "date": "2026-06-05T23:17:27.000Z", "commit": "4b2364fa5f8c2871acddf90eb8104d5fb6d26ee8", "fileid": "b37db4fbcd349618030ca1e7ff2b40c27f44d4132733c219a4e24e4558771729", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/k96nb01/actions/runs/27044983752" } ] }