{ "_id": "6a1afec81d7bb097a09fecb6", "Package": "HLAtools", "Type": "Package", "Title": "Toolkit for HLA Immunogenomics", "Version": "1.8.1", "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. 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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", "Molecular Characteristics of HLA Region Genes", "Gazetteer of HLA Region Genes", "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", "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": "2026-05-30 06:46:15", "commits": 52 } ], "_score": 5.658964842664435, "_indexed": true, "_nocasepkg": "hlatools", "_universes": [ "sjmack" ], "_previous": "1.8.0", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.8.1", "date": "2026-05-30T10:47:32.000Z", "distro": "noble", "commit": "edc9cdc1de112ba8a74e3eed7d9bb069c79e90f1", "fileid": "51cc3ce1018faaecaf564b112e7a041ba274de703c938894886ee7b27ce81c3b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/sjmack/actions/runs/26680307690" }, { "r": "4.6.0", "os": "linux", "version": "1.8.1", "date": "2026-05-30T10:47:43.000Z", "distro": "noble", "commit": "edc9cdc1de112ba8a74e3eed7d9bb069c79e90f1", "fileid": "261ef9532c161b7f4b87e50b3fd2528478155e3b35c8298635c70039e78cfca0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/sjmack/actions/runs/26680307690" }, { "r": "4.5.3", "os": "mac", "version": "1.8.1", "date": "2026-05-30T15:13:07.000Z", "commit": "edc9cdc1de112ba8a74e3eed7d9bb069c79e90f1", "fileid": "a45b0a200b96e8d8936d097ec99913bb162b32b9ff7d78b0095de58bf2e3d339", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/sjmack/actions/runs/26680307690" }, { "r": "4.6.0", "os": "mac", "version": "1.8.1", "date": "2026-05-30T15:12:17.000Z", "commit": "edc9cdc1de112ba8a74e3eed7d9bb069c79e90f1", "fileid": "53d45973b32ff3dc952901edd50d79a5e7bc44168629d4a2db1f60bd2955a1eb", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/sjmack/actions/runs/26680307690" }, { "r": "4.6.0", "os": "wasm", "version": "1.8.1", "date": "2026-05-30T10:47:30.000Z", "commit": "edc9cdc1de112ba8a74e3eed7d9bb069c79e90f1", "fileid": "ad76b8f4449618d6a456c9274a2ebf5894b63c25b7f15e658865129ed03779b4", "status": "success", "buildurl": "https://github.com/r-universe/sjmack/actions/runs/26680307690" }, { "r": "4.7.0", "os": "win", "version": "1.8.1", "date": "2026-05-30T10:46:35.000Z", "commit": "edc9cdc1de112ba8a74e3eed7d9bb069c79e90f1", "fileid": "80da05cb199f813952abbbda42fc0c2ec19c60b6cc55a49d0f41adc3af3c361f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/sjmack/actions/runs/26680307690" }, { "r": "4.5.3", "os": "win", "version": "1.8.1", "date": "2026-05-30T10:46:23.000Z", "commit": "edc9cdc1de112ba8a74e3eed7d9bb069c79e90f1", "fileid": "68270ba75163e9b8e5a612de832b184455c9a0818070a8b6013ff0af2eea79d5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/sjmack/actions/runs/26680307690" }, { "r": "4.6.0", "os": "win", "version": "1.8.1", "date": "2026-05-30T10:46:37.000Z", "commit": "edc9cdc1de112ba8a74e3eed7d9bb069c79e90f1", "fileid": "c326bef415623ebd7cea7464222190b84b4bb87999bba6b68b3fad28f4c98edf", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/sjmack/actions/runs/26680307690" } ] }