{ "_id": "6acd6a65a14063b82c3ab3c1", "Package": "HLAtools", "Type": "Package", "Title": "Toolkit for HLA Immunogenomics", "Version": "1.18.0", "Authors@R": "c(person(\"Livia\", \"Tran\", , \"livia.tran@ucsf.edu\", role = c(\"aut\")),\nperson(\"Ryan\", \"Nickens\", , \"rynickens@gmail.com\", role = c(\"aut\")),\nperson(\"Leamon\", \"Crooms IV\", , \"lcroomsiv@gmail.com\", role = \"aut\"),\nperson(\"Derek\", \"Pappas\", , \"djpappas75@gmail.com\", role = \"aut\"),\nperson(\"Vinh\", \"Luu\", , \"vinhluu864@berkeley.edu\", role = \"ctb\"),\nperson(\"Josh\", \"Bredeweg\", , role = \"ctb\"),\nperson(\"Steven\", \"Mack\", , \"Steven.Mack@ucsf.edu\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-9820-9547\")))", "Maintainer": "Steven Mack ", "Description": "A toolkit for the analysis and management of data for\ngenes in the so-called \"Human Leukocyte Antigen\" (HLA) region.\nFunctions extract reference data from the Anthony Nolan HLA\nInformatics Group/ImmunoGeneTics HLA 'GitHub' repository\n(ANHIG/IMGTHLA) , validate\nGenotype List (GL) Strings, convert between UNIFORMAT and GL\nString Code (GLSC) formats, translate HLA alleles and GLSCs\nacross ImmunoPolymorphism Database (IPD) IMGT/HLA Database\nrelease versions, identify differences between pairs of alleles\nat a locus, generate customized, multi-position sequence\nalignments, trim and convert allele-names across nomenclature\nepochs, and extend existing data-analysis methods. Tran et al.,\n(2025) .", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "LazyData": "true", "LazyDataCompression": "xz", "Config/testthat/edition": "3", "VignetteBuilder": "knitr", "License": "GPL (>= 3)", "URL": "", "Config/roxygen2/version": "8.1.0", "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev libxml2-dev\nlibssl-dev libx11-dev zlib1g-dev", "Repository": "https://sjmack.r-universe.dev", "Date/Publication": "2026-10-12 17:10:51 UTC", "RemoteUrl": "https://github.com/sjmack/hlatools", "RemoteRef": "HEAD", "RemoteSha": "2be9b94c57edbd320b4b709327b2899180fb60ac", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-12 23:10:43 UTC", "User": "root" }, "Author": "Livia Tran [aut],\nRyan Nickens [aut],\nLeamon Crooms IV [aut],\nDerek Pappas [aut],\nVinh Luu [ctb],\nJosh Bredeweg [ctb],\nSteven Mack [aut, cre] (ORCID: )", "_user": "sjmack", "_type": "src", "_file": "HLAtools_1.18.0.tar.gz", "_fileid": "https://r2.ropensci.org/b92e8a145d580647dd7cdb49c445c8fcd4edc3d6201d4505ec8baed0586a5217", "_filesize": 5568624, "_sha256": "b92e8a145d580647dd7cdb49c445c8fcd4edc3d6201d4505ec8baed0586a5217", "_expires": "2027-01-20T23:16:50.000Z", "_created": "2026-10-12T23:10:43.000Z", "_published": "2026-10-12T23:16:52.959Z", "_buildurl": "https://github.com/r-universe/sjmack/actions/runs/38320372105", "_status": "success", "_host": "GitHub-Actions", "_jobs": [ { "job": 115048157868, "time": 219, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11778633235" }, { "job": 115048157825, "time": 217, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11778094151" }, { "job": 115048157878, "time": 179, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "11778462208" }, { "job": 115048157929, "time": 151, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11778338540" }, { "job": 115046864434, "time": 273, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11778421864" }, { "job": 115048157803, "time": 129, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11778663041" }, { "job": 115048157832, "time": 146, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11778338513" }, { "job": 115048157817, "time": 130, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "11778981702" }, { "job": 115048157945, "time": 130, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11778672973" } ], "_upstream": "https://github.com/sjmack/hlatools", "_commit": { "id": "2be9b94c57edbd320b4b709327b2899180fb60ac", "author": "sjmack ", "committer": "sjmack ", "message": "Version 1.18 October 12, 2026\n- Remove deprecated 'fill = TRUE' from html_table() calls in extractGenomicReferenceGenes() and extractGeneTypes(). Thanks to Hadley Wickham for the PR.\n- Add the genomicReferencesLookup() function, for looking up Genomic Reference data for each locus in the IMGTGenomicReferences$GenomicReferences data object.\n- Add the queryAlleleStatus(), multiQueryAlleleStatus(), alleleStatusLookup(), alleleStatusSummary() and validationByTranslation() functions, for working with the alleleStatus$AlleleStatus table, with associated updates to package documentation.\n- Update the URL pointing to information about the BIGDAWG data format to \"https://github.com/IgDAWG/BIGDAWG/blob/main/vignettes/BIGDAWG.Rmd\" in the documentation for relRisk() and BDstrat(), and in the package vignette.\n- Add the queryRelDNASer(), relDNASerLookup(), relSerSerLookup(), appendWMDA(), expandAntigenTerms() and flattenTable() functions for working with the WMDASerologicalRelationships$rel_dna_ser and $rel_ser_ser tables.\n- Add the buildWMDASerRel() function, which generates the WMDASerologicalRelationships object.\n- Add the WMDASerologicalRelationships object to global variables.\n- Update compareSequences() to correctly identify cases when there are no differences or one difference between the specified alleles for a given 'alignType'.\n", "time": 1791825051 }, "_maintainer": { "name": "Steven Mack", "email": "steven.mack@ucsf.edu", "login": "sjmack", "orcid": "0000-0001-9820-9547", "description": "", "uuid": 8935284 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.6.0", "role": "Depends" }, { "package": "DescTools", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "fmsb", "role": "Imports" }, { "package": "rvest", "version": ">= 1.0.0", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "xfun", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "sjmack", "_selfowned": true, "_usedby": 1, "_updates": [ { "week": "2026-14", "n": 1 }, { "week": "2026-22", "n": 6 }, { "week": "2026-25", "n": 3 }, { "week": "2026-30", "n": 1 }, { "week": "2026-31", "n": 1 }, { "week": "2026-42", "n": 2 } ], "_tags": [], "_stars": 4, "_contributors": [ { "user": "sjmack", "count": 180, "uuid": 8935284 }, { "user": "tranlivia", "count": 2, "uuid": 105305038 }, { "user": "hadley", "count": 1, "uuid": 4196 } ], "_userbio": { "uuid": 8935284, "type": "user", "name": "Steve Mack", "followers": 12 }, "_downloads": { "count": 450, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/HLAtools" }, "_devurl": "https://github.com/sjmack/hlatools", "_searchresults": 31, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/HLAtools.html", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md" ], "_homeurl": "https://github.com/sjmack/hlatools", "_realowner": "sjmack", "_cranurl": true, "_releases": [ { "version": "1.1.1", "date": "2024-07-26" }, { "version": "1.2.0", "date": "2024-09-02" }, { "version": "1.3.0", "date": "2024-11-14" }, { "version": "1.4.0", "date": "2025-03-03" }, { "version": "1.6.2", "date": "2025-05-01" }, { "version": "1.6.3", "date": "2025-07-21" }, { "version": "1.11.0", "date": "2026-07-22" } ], "_exports": [ "addCodonLine", "alignmentFull", "alignmentSearch", "alleleStatusLookup", "alleleStatusSummary", "alleleTrim", "appendWMDA", "atlasFull", "atlasMaker", "BDstrat", "BDtoPyPop", "buildAlignments", "buildGazetteer", "buildGenomicReferences", "buildIMGTHLAGeneTypes", "buildWMDASerRel", "checkAlignType", "checkgDNAstart", "checkSource", "checkVersion", "compareSequences", "convertAny", "countSpaces", "customAlign", "expandAntigenTerms", "expandVersion", "ffN", "flattenTable", "formatHead", "genomicReferencesLookup", "getAlignmentNames", "getField", "getLatestVersion", "GIANT", "GLStoUNI", "GLtoUN", "GLupdate", "GLV", "GLV2", "GLvalidate", "GLVhelper", "motifMatch", "multiAlign", "multiAlleleTrim", "multiGLStoUNI", "multiLocusValidation", "multiQueryAlleleStatus", "multiQueryRelease", "multiSearch", "multiTranslateGLstring", "multiUNItoGLS", "multiUpdateGL", "numFields", "parseAlignmentHead", "posSort", "pypopHeaders", "queryAlleleStatus", "queryPositions", "queryRelDNASer", "queryRelease", "redec", "relDNASerLookup", "relRisk", "relSerSerLookup", "repoVersion", "squashVersion", "translateAllele", "translateGLstring", "typeToSource", "uniAlign", "uniSearch", "UNItoGLS", "UNtoGL", "updateAll", "updateAlleleListHistory", "updateAlleleStatus", "updateGL", "validateAllele", "validateGLstring", "validateLocus", "validateMotif", "validatePositions", "validateUniformat", "validateVersion", "validationByTranslation", "variantTable", "verifyAllele" ], "_datasets": [ { "name": "alleleListHistory", "title": "Allele Names Across All Release Versions", "object": "alleleListHistory", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "alleleStatus", "title": "Key data for each allele in the IPD-IMGT/HLA Database. A list object consisting of two elements - $AlleleStatus and $version. This object is built by the updateAlleleStatus() function.", "object": "alleleStatus", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "fragmentFeatureNames", "title": "Gene Features of HLA Pseudogenes and Gene Fragments", "object": "fragmentFeatureNames", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "GLSC.ex", "title": "Example Data Frame of Genotype List String Code Data", "object": "GLSC.ex", "class": [ "data.frame" ], "fields": [ "Relation", "GL.String.Code" ], "rows": 419, "table": true, "tojson": true }, { "name": "GLstring.ex", "title": "Example Data Frame of Genotype List String Data.", "object": "GLstring.ex", "class": [ "data.frame" ], "fields": [ "Relation", "Gl.String" ], "rows": 419, "table": true, "tojson": true }, { "name": "HLAatlas", "title": "Boundary Positions of Exons, Introns and UTRs in Amino Acid, cDNA and gDNA Alignments", "object": "HLAatlas", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "HLAgazetteer", "title": "Functional and Organizational Categories of Genes Supported by the IPD-IMGT/HLA Database", "object": "HLAgazetteer", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "IMGTGenomicReferences", "title": "Genomic Reference Alleles for each Gene in the IPD-IMGT/HLA Database", "object": "IMGTGenomicReferences", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "IMGTHLAGeneTypes", "title": "Molecular characteristics of the Genes Curated by the IPD-IMGT/HLA Database", "object": "IMGTHLAGeneTypes", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "sHLAdata", "title": "Synthetic HLA Data for use with Package Examples", "object": "sHLAdata", "class": [ "data.frame" ], "fields": [ "Subject", "Status", "A", "A", "C", "C", "B", "B", "DRB1", "DRB1", "DQA1", "DQA1", "DQB1", "DQB1", "DPA1", "DPA1", "DPB1", "DPB1" ], "rows": 47, "table": true, "tojson": true }, { "name": "UNIFORMAT.example", "title": "Example Data Frame of UNIFORMAT Data.", "object": "UNIFORMAT.example", "class": [ "data.frame" ], "fields": [ "sample.id", "genotype" ], "rows": 20, "table": true, "tojson": true }, { "name": "WMDASerologicalRelationships", "title": "Descriptions of relationships between serologically defined HLA antigens and HLA alleles. rel_ser_ser describes relationships between all defined antigens, broad antigens, split antigens and associated antigens. rel_dna_ser describes the known unambiguous, possible or seorlogically equivalent antigen for each HLA allele.", "object": "WMDASerologicalRelationships", "class": [ "list" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "addCodonLine", "title": "Add an 'AA codon' Line to Alignments When Missing.", "topics": [ "addCodonLine" ] }, { "page": "alignmentFull", "title": "Build Sets of Protein, Codon, Coding Nucleotide and Genomic Nucleotide Alignments for Specified Loci", "topics": [ "alignmentFull" ] }, { "page": "alignmentSearch", "title": "Search Alignments for Specific Positions in a Specific Allele", "topics": [ "alignmentSearch" ] }, { "page": "alleleListHistory", "title": "Allele Names Across All Release Versions", "topics": [ "alleleListHistory" ] }, { "page": "alleleStatus", "title": "Key data for each allele in the IPD-IMGT/HLA Database. A list object consisting of two elements - $AlleleStatus and $version. This object is built by the updateAlleleStatus() function.", "topics": [ "alleleStatus" ] }, { "page": "alleleStatusLookup", "title": "#'Lookup alleles that share alleleStatus$AlleleStatus table values", "topics": [ "alleleStatusLookup" ] }, { "page": "alleleStatusSummary", "title": "Identify the unique values in the alleleStatus table", "topics": [ "alleleStatusSummary" ] }, { "page": "alleleTrim", "title": "Trim All Versions of HLA Allele Names", "topics": [ "alleleTrim" ] }, { "page": "appendWMDA", "title": "Increase Searchability of WMDASerologicalRelationships's rel_dna_ser table", "topics": [ "appendWMDA" ] }, { "page": "atlasFull", "title": "Generate a Complete set of Protein, Coding nucleotide and Genomic Nucleotide Atlases", "topics": [ "atlasFull" ] }, { "page": "atlasMaker", "title": "Identify the Gene-Feature Boundaries in HLA Region Genes", "topics": [ "atlasMaker" ] }, { "page": "BDstrat", "title": "Stratify BIGDAWG Datasets by Specific Alleles", "topics": [ "BDstrat" ] }, { "page": "BDtoPyPop", "title": "Convert BIGDAWG datasets to PyPop datasets Converts a BIGDAWG-formatted data frame into a pair of PyPop-formatted case and control data frames.", "topics": [ "BDtoPyPop" ] }, { "page": "buildAlignments", "title": "Build Amino Acid, cDNA and gDNA Alignments", "topics": [ "buildAlignments" ] }, { "page": "buildGazetteer", "title": "Define Categories of Genes Supported by the IPD-IMGT/HLA Database", "topics": [ "buildGazetteer" ] }, { "page": "buildGenomicReferences", "title": "Generate a Table of Genomic Reference Alleles and Characteristics of HLA Genes Defined by the IPD-IMGT/HLA Database", "topics": [ "buildGenomicReferences" ] }, { "page": "buildIMGTHLAGeneTypes", "title": "Describe IPD-IMGT/HLA Database Genes, Identifying Pseudogenes and Gene Fragments", "topics": [ "buildIMGTHLAGeneTypes" ] }, { "page": "buildWMDASerRel", "title": "Build local copies of the rel_ser_ser and rel_dna_ser tables.", "topics": [ "buildWMDASerRel" ] }, { "page": "checkAlignType", "title": "Ensure that AlignType Values are Valid", "topics": [ "checkAlignType" ] }, { "page": "checkgDNAstart", "title": "Identify gDNA Alignments in Which the First Feature Boundary is not Identified as Position +1.", "topics": [ "checkgDNAstart" ] }, { "page": "checkSource", "title": "Ensure that Source Values are Valid", "topics": [ "checkSource" ] }, { "page": "checkVersion", "title": "Check IPD-IMGT/HLA Release Version Allele Names", "topics": [ "checkVersion" ] }, { "page": "compareSequences", "title": "Identify Sequence Differences Between Two Alleles", "topics": [ "compareSequences" ] }, { "page": "convertAny", "title": "Convert Values Across an Entire Data Frame or Vector", "topics": [ "convertAny" ] }, { "page": "countSpaces", "title": "Count the Spaces in a Character String", "topics": [ "countSpaces" ] }, { "page": "customAlign", "title": "Generate a Customized Peptide, Codon or Nucleotide Sequence Alignment.", "topics": [ "customAlign" ] }, { "page": "expandAntigenTerms", "title": "Reformat the rel_ser_ser and rel_dna_ser tables to enable searches within slash-delimited strings of antigen terms.", "topics": [ "expandAntigenTerms" ] }, { "page": "expandVersion", "title": "Add 'Dot' Delimiters to a Numeric Release Version", "topics": [ "expandVersion" ] }, { "page": "ffN", "title": "Identify and Annotate Gene Features in Pseudogenes and Gene Fragments.", "topics": [ "ffN" ] }, { "page": "flattenTable", "title": "Reduce a mulirow data.frame of antigen data to a single row.", "topics": [ "flattenTable" ] }, { "page": "formatHead", "title": "Format PyPop Data Frame Headers", "topics": [ "formatHead" ] }, { "page": "fragmentFeatureNames", "title": "Gene Features of HLA Pseudogenes and Gene Fragments", "topics": [ "fragmentFeatureNames" ] }, { "page": "genomicReferencesLookup", "title": "Searches the IMGTGenomicReferences$GenomicReferences table to return genomic reference data for specific IPD-IMGT/HLA genes.", "topics": [ "genomicReferencesLookup" ] }, { "page": "getAlignmentNames", "title": "Retrieve Alignment Filenames for HLA Genes", "topics": [ "getAlignmentNames" ] }, { "page": "GetField", "title": "Trim Colon-Delimited HLA Allele Names by Field", "topics": [ "getField" ] }, { "page": "getLatestVersion", "title": "Identify the Latest IPD-IMGT/HLA Database Release", "topics": [ "getLatestVersion" ] }, { "page": "GIANT", "title": "GL string code-Integrated Allele Name Translation", "topics": [ "GIANT" ] }, { "page": "GLSC.ex", "title": "Example Data Frame of Genotype List String Code Data", "topics": [ "GLSC.ex" ] }, { "page": "GLStoUNI", "title": "Translate GL String to UNIFORMAT", "topics": [ "GLStoUNI" ] }, { "page": "GLstring.ex", "title": "Example Data Frame of Genotype List String Data.", "topics": [ "GLstring.ex" ] }, { "page": "GLtoUN", "title": "Translate GL Strings to UNIFORMAT Strings", "topics": [ "GLtoUN" ] }, { "page": "GLupdate", "title": "Update a GL String Code to a Specified IPD-IMGT/HLA Database Version", "topics": [ "GLupdate" ] }, { "page": "GLV", "title": "Retrieve Version from Input GL String", "topics": [ "GLV" ] }, { "page": "GLV2", "title": "Format GL String Code Version Number", "topics": [ "GLV2" ] }, { "page": "GLvalidate", "title": "Validate a GL String Code", "topics": [ "GLvalidate" ] }, { "page": "GLVhelper", "title": "Locate Matches for an Incomplete IPD-IMGT/HLA Database Version", "topics": [ "GLVhelper" ] }, { "page": "HLAatlas", "title": "Boundary Positions of Exons, Introns and UTRs in Amino Acid, cDNA and gDNA Alignments", "topics": [ "HLAatlas" ] }, { "page": "HLAgazetteer", "title": "Functional and Organizational Categories of Genes Supported by the IPD-IMGT/HLA Database", "topics": [ "HLAgazetteer" ] }, { "page": "IMGTGenomicReferences", "title": "Genomic Reference Alleles for each Gene in the IPD-IMGT/HLA Database", "topics": [ "IMGTGenomicReferences" ] }, { "page": "IMGTHLAGeneTypes", "title": "Molecular characteristics of the Genes Curated by the IPD-IMGT/HLA Database", "topics": [ "IMGTHLAGeneTypes" ] }, { "page": "motifMatch", "title": "Identify Alleles that Share a Sequence Motif", "topics": [ "motifMatch" ] }, { "page": "multiAlign", "title": "Generate an Alignment for Specific Alleles at Different Positions", "topics": [ "multiAlign" ] }, { "page": "multiAlleleTrim", "title": "Trim Multiple HLA Allele Names", "topics": [ "multiAlleleTrim" ] }, { "page": "multiGLStoUNI", "title": "Translate Multiple GL Strings to UNIFORMAT", "topics": [ "multiGLStoUNI" ] }, { "page": "multiLocusValidation", "title": "Apply validateLocus() to Multiple Loci", "topics": [ "multiLocusValidation" ] }, { "page": "multiQueryAlleleStatus", "title": "Query the the allele status data for multiple alleles.", "topics": [ "multiQueryAlleleStatus" ] }, { "page": "multiQueryRelease", "title": "Search Multiple Elements of Allele Names Across Release Versions", "topics": [ "multiQueryRelease" ] }, { "page": "multiSearch", "title": "Search Alignment Sequences at Multiple Positions for a Specified Allele", "topics": [ "multiSearch" ] }, { "page": "multiTranslateGLstring", "title": "Translate a Vector of GL Strings to a Desired IPD-IMGT/HLA Database Version", "topics": [ "multiTranslateGLstring" ] }, { "page": "multiUNItoGLS", "title": "Translate Multiple UNIFORMAT Strings to GL Strings", "topics": [ "multiUNItoGLS" ] }, { "page": "multiUpdateGL", "title": "Update a Vector of GL String Code Data to a Desired IPD-IMGT/HLA Database Version", "topics": [ "multiUpdateGL" ] }, { "page": "numFields", "title": "Identify the Number of Fields in a Colon-Delimited Allele Name", "topics": [ "numFields" ] }, { "page": "parseAlignmentHead", "title": "Guides for Parsing the Header Blocks of Alignment Files", "topics": [ "parseAlignmentHead" ] }, { "page": "posSort", "title": "Numerical Sort of Alignment Positions that Contain Indels", "topics": [ "posSort" ] }, { "page": "pypopHeaders", "title": "Convert BIGDAWG File Headers to PyPop Format", "topics": [ "pypopHeaders" ] }, { "page": "queryAlleleStatus", "title": "Query the allele status data for a particular allele in the alleleStatus$AlleleStatus data object.", "topics": [ "queryAlleleStatus" ] }, { "page": "queryPositions", "title": "Extract Variant Information for Specific Positions in an Alignment", "topics": [ "queryPositions" ] }, { "page": "queryRelDNASer", "title": "Query the WMDASerologialRelationships$rel_dna_ser table values for a specific allele", "topics": [ "queryRelDNASer" ] }, { "page": "queryRelease", "title": "Search Allele Names Across Release Versions", "topics": [ "queryRelease" ] }, { "page": "redec", "title": "Reintroduce Version Decimals", "topics": [ "redec" ] }, { "page": "relDNASerLookup", "title": "Lookup alleles that share WMDASerologialRelationships$rel_dna_ser table values", "topics": [ "relDNASerLookup" ] }, { "page": "relRisk", "title": "Calculate Relative Risk for Individual Alleles and Genotypes in BIGDAWG-formatted Non-Case-Control Datasets", "topics": [ "relRisk" ] }, { "page": "relSerSerLookup", "title": "Lookup a specific antigen, split antigen or associated antigen, and identify the values for the other two", "topics": [ "relSerSerLookup" ] }, { "page": "repoVersion", "title": "Convert an AlleleListHistory Release Version to the GitHub Repository Version", "topics": [ "repoVersion" ] }, { "page": "sHLAdata", "title": "Synthetic HLA Data for use with Package Examples", "topics": [ "sHLAdata" ] }, { "page": "squashVersion", "title": "Reduce a Release Version to Numerals", "topics": [ "squashVersion" ] }, { "page": "translateAllele", "title": "Translate HLA Allele Names across IPD-IMGT/HLA Database Release Versions", "topics": [ "translateAllele" ] }, { "page": "translateGLstring", "title": "Translate a GL String across IPD-IMGT/HLA Database Release Versions", "topics": [ "translateGLstring" ] }, { "page": "typeToSource", "title": "Convert AlignType Values to Source Values", "topics": [ "typeToSource" ] }, { "page": "uniAlign", "title": "Generate an Alignment for Specific Alleles at Specific Positions", "topics": [ "uniAlign" ] }, { "page": "UNIFORMAT.example", "title": "Example Data Frame of UNIFORMAT Data.", "topics": [ "UNIFORMAT.example" ] }, { "page": "uniSearch", "title": "Search Sequences at a Single Position for an Allele", "topics": [ "uniSearch" ] }, { "page": "UNItoGLS", "title": "Translate UNIFORMAT to GL String", "topics": [ "UNItoGLS" ] }, { "page": "UNtoGL", "title": "Translate UNIFORMAT Strings to GL Strings", "topics": [ "UNtoGL" ] }, { "page": "updateAll", "title": "Update All Package Data Objects Derived from IPD-IMGT/HLA Database Resources", "topics": [ "updateAll" ] }, { "page": "updateAlleleListHistory", "title": "Build the AlleleList History R Object", "topics": [ "updateAlleleListHistory" ] }, { "page": "updateAlleleStatus", "title": "Build the alleleStatus object", "topics": [ "updateAlleleStatus" ] }, { "page": "updateGL", "title": "Update a GL String Code to a Specified IPD-IMGT/HLA Database Version", "topics": [ "updateGL" ] }, { "page": "validateAllele", "title": "Validate Allele-Name Format and Presence in HLAalignments", "topics": [ "validateAllele" ] }, { "page": "validateGLstring", "title": "Validate a GL String", "topics": [ "validateGLstring" ] }, { "page": "validateLocus", "title": "Determine if a Locus Name is in the HLAgazetteer", "topics": [ "validateLocus" ] }, { "page": "validateMotif", "title": "Determine if a Motif is Properly Formatted", "topics": [ "validateMotif" ] }, { "page": "validatePositions", "title": "Validate the Presence of Variant Positions in an Alignment", "topics": [ "validatePositions" ] }, { "page": "validateUniformat", "title": "Validate a UNIFORMAT String", "topics": [ "validateUniformat" ] }, { "page": "validateVersion", "title": "Validate an IPD-IMGT/HLA Release Version", "topics": [ "validateVersion" ] }, { "page": "validationByTranslation", "title": "Validate an HLA allele name by attempting to translate it to its most recent version.", "topics": [ "validationByTranslation" ] }, { "page": "variantTable", "title": "Builds a Data Frame of Variant Information for Specific Positions in an Alignment", "topics": [ "variantTable" ] }, { "page": "verifyAllele", "title": "Determine if an Allele Name Ever Existed, and (if so) in Which IPD-IMGT/HLA Database Releases", "topics": [ "verifyAllele" ] }, { "page": "WMDASerologicalRelationships", "title": "Descriptions of relationships between serologically defined HLA antigens and HLA alleles. rel_ser_ser describes relationships between all defined antigens, broad antigens, split antigens and associated antigens. rel_dna_ser describes the known unambiguous, possible or seorlogically equivalent antigen for each HLA allele.", "topics": [ "WMDASerologicalRelationships" ] } ], "_readme": "https://github.com/sjmack/hlatools/raw/HEAD/README.md", "_rundeps": [ "askpass", "bit", "bit64", "boot", "cellranger", "class", "cli", "clipr", "cpp11", "crayon", "curl", "data.table", "DescTools", "dplyr", "e1071", "Exact", "expm", "fmsb", "forcats", "fs", "generics", "gld", "glue", "haven", "hms", "httr", "jsonlite", "lattice", "lifecycle", "lmom", "magrittr", "MASS", "Matrix", "mime", "mvtnorm", "openssl", "pillar", "pkgconfig", "prettyunits", "progress", "proxy", "R6", "Rcpp", "readr", "readxl", "rematch", "rlang", "rootSolve", "rstudioapi", "rvest", "selectr", "stringi", "stringr", "sys", "tibble", "tidyselect", "tzdb", "utf8", "vctrs", "vroom", "withr", "xfun", "xml2" ], "_vignettes": [ { "source": "HLAtools.Rmd", "filename": "HLAtools.html", "title": "HLAtools", "author": "Ryan Nickens -- rynickens@gmail.com, Livia Tran -- livia.tran@ucsf.edu, Leamon Crooms IV -- lcroomsiv@gmail.com, Derek Pappas, PhD -- djpappas75@gmail.com, Vinh Luu -- vinhluu864@berkeley.edu, Josh Bredeweg, Steven J. Mack, PhD -- steven.mack@ucsf.edu", "engine": "knitr::rmarkdown", "headings": [ "Overview", "1. Reference Datasets", "Atlas of Gene Feature Boundaries", "Protein Sequence Atlases", "Nucleotide Sequence Atlases", "Genomic Sequence Atlases", "Historical Catalogue of HLA Allele Names", "Functional and Organizational Categories of Genes in the HLA Region", "Key Characteristics of Each HLA Region Gene", "Molecular Characteristics of HLA Region Genes", "Gazetteer of HLA Region Genes", "Genomic Reference Alleles", "Relationships between HLA Alleles and Antigens", "Annotation of Pseudogene and Gene Fragment Features", "Sequence Alignments", "Protein (AA) Aligments", "Codon and Individual Nucleotide (cDNA) Sequence Alignments", "Genomic (gDNA) Sequence Alignments", "Insertion-Deletion (Indel) Variant Representation", "2. Working with Sequence Alignments", "Building Alignments", "Working with Alignments in Past Releases", "Caveats for Alignments from Previous Releases", "3. Trim, Search and Query Functions", "Trimming HLA Allele Names by Digits or Fields", "Identifying Differences Between Alleles at a Locus", "Searching Allele Names Across IPD-IMGT/HLA Database Release Versions", "Searching Alignments at Specific Positions", "Identifying Sequence Variants at Specific Positions and their Frequencies Across all Alleles", "Searching Alignments for Sequence Motifs", "Searching the WMDA's rel_dna_ser and rel_ser_ser Tables", "Search, Query and Look-up data in the AlleleStatus data object", "Look-up genomic reference data data in the genomicReferences data object", "Building Custom Alignments", "4. Data Translation and Conversion Tools", "Working with Genotype List String (GL String), GL String Code (GLSC), and UNIFORMAT Data", "Translate GL String Codes Across IPD-IMGT/HLA Database Release Versions", "updateGL", "multiUpdateGL", "Translate vectors and data frames of HLA allele name data across IPD-IMGT/HLA Database Release Versions", "Convert GL String-formatted data to UNIFORMAT-formatted data", "validateGLstring", "GLStoUNI", "multiGLStoUNI", "Convert UNIFORMAT-formatted data to GL String-formatted data", "validateUniformat", "UNItoGLS", "multiUNItoGLS", "5. Data Analysis Tools", "Example Data", "Calculating Relative Risk with BIGDAWG-formatted Datasets", "relRisk", "Division of BIGDAWG-formatted Datasets for Stratification Analyses", "BDstrat: Multilocus Allele Stratification for BIGDAWG Datasets", "Conversion of BIGDAWG-formatted Datasets to Python for Population Genetics (PyPop)-formatted Datasets", "BDtoPyPop : Enabling Population Genetic Analyses of Case and Control Datasets" ], "created": "2024-03-25 22:20:20", "modified": "2026-10-12 17:10:51", "commits": 56 } ], "_score": 6.348694190265541, "_indexed": true, "_nocasepkg": "hlatools", "_universes": [ "sjmack" ], "_previous": "1.12.0", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.18.0", "date": "2026-10-12T23:13:48.000Z", "distro": "resolute", "commit": "2be9b94c57edbd320b4b709327b2899180fb60ac", "fileid": "https://r2.ropensci.org/9cd13345a96161fbd7347eea1e83466850fb89c8f7871ef2d7026e90910e59ed", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/sjmack/actions/runs/38320372105" }, { "r": "4.6.1", "os": "linux", "version": "1.18.0", "date": "2026-10-12T23:13:59.000Z", "distro": "resolute", "commit": "2be9b94c57edbd320b4b709327b2899180fb60ac", "fileid": "https://r2.ropensci.org/3a48317fed000a269184ace0514e58d275cfee433a2bbeac33402866d72aef81", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/sjmack/actions/runs/38320372105" }, { "r": "4.5.3", "os": "mac", "version": "1.18.0", "date": "2026-10-12T23:13:05.000Z", "commit": "2be9b94c57edbd320b4b709327b2899180fb60ac", "fileid": "https://r2.ropensci.org/2dfec8797071fff1bdf504df4fd7af717562569ee02e6e73148ee3d4c901f6d2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/sjmack/actions/runs/38320372105" }, { "r": "4.6.1", "os": "mac", "version": "1.18.0", "date": "2026-10-12T23:12:57.000Z", "commit": "2be9b94c57edbd320b4b709327b2899180fb60ac", "fileid": "https://r2.ropensci.org/e8dcf61d569861b6901a42c26c9820868654edda9254aab3b2c647e2ae5a79a7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/sjmack/actions/runs/38320372105" }, { "r": "4.6.0", "os": "wasm", "version": "1.18.0", "date": "2026-10-12T23:13:18.000Z", "commit": "2be9b94c57edbd320b4b709327b2899180fb60ac", "fileid": "https://r2.ropensci.org/f2351ef09fca11372b9280a1fc23dd47a48dabd5212d57467262fad169c3b571", "status": "success", "buildurl": "https://github.com/r-universe/sjmack/actions/runs/38320372105" }, { "r": "4.7.0", "os": "win", "version": "1.18.0", "date": "2026-10-12T23:12:18.000Z", "commit": "2be9b94c57edbd320b4b709327b2899180fb60ac", "fileid": "https://r2.ropensci.org/c2b83680eef8014f84b9fb742ad348bdde7c898d1eb95f3294872f366ea5e95a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/sjmack/actions/runs/38320372105" }, { "r": "4.5.3", "os": "win", "version": "1.18.0", "date": "2026-10-12T23:12:11.000Z", "commit": "2be9b94c57edbd320b4b709327b2899180fb60ac", "fileid": "https://r2.ropensci.org/735c56c7c685fdb6bf7f62c353ddbc994b93ad2b196a7be8d07c215fe01b0a12", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/sjmack/actions/runs/38320372105" }, { "r": "4.6.1", "os": "win", "version": "1.18.0", "date": "2026-10-12T23:12:16.000Z", "commit": "2be9b94c57edbd320b4b709327b2899180fb60ac", "fileid": "https://r2.ropensci.org/b0f8bd2be48e25a77c7ae891d421b42e080c7862c830208c9051ce3828f21923", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/sjmack/actions/runs/38320372105" } ] }