{ "_id": "6aaf8b3a3d719c1f8407eb42", "Package": "hlaR", "Type": "Package", "Title": "Tools for HLA Data", "Version": "1.0.0", "Description": "A streamlined tool for eplet analysis of donor and\nrecipient HLA (human leukocyte antigen) mismatch. Messy,\nlow-resolution HLA typing data is cleaned, and imputed to\nhigh-resolution using the NMDP (National Marrow Donor Program)\nhaplotype reference database\n. High resolution data is\nanalyzed for overall or single antigen eplet mismatch using a\nreference table (currently supporting 'HLAMatchMaker'\n versions 2 and 3). Data can enter or\nexit the workflow at different points depending on the user's\naims and initial data quality.", "Authors@R": "c(person(\"Joan\",\"Zhang\",email = \"joan.zhang@emory.edu\", role = c(\"aut\", \"cre\")),\nperson(\"Aileen\",\"Johnson\",email = \"aileen.johnson@emory.edu \", role = c(\"aut\")),\nperson(\"Christian P\",\"Larsen\",email = \"clarsen@emory.edu\", role = c(\"cph\", \"aut\")))", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "RoxygenNote": "7.2.2", "URL": "https://pubmed.ncbi.nlm.nih.gov/35101308/,\nhttps://emory-larsenlab.shinyapps.io/hlar_shiny/", "BugReports": "https://github.com/LarsenLab/hlaR/issues", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "cmake libfontconfig1-dev libfreetype6-dev\nlibfribidi-dev git make libharfbuzz-dev libgit2-dev libicu-dev\nlibjpeg-dev libpng-dev libtiff-dev libuv1-dev libwebp-dev\nlibxml2-dev libssl-dev libx11-dev zlib1g-dev", "Repository": "https://larsenlab.r-universe.dev", "Date/Publication": "2023-03-02 21:38:22 UTC", "RemoteUrl": "https://github.com/larsenlab/hlar", "RemoteRef": "HEAD", "RemoteSha": "a7fec958e00d3a7b00f5128900c6b328c2bcb75c", "NeedsCompilation": "no", "Packaged": { "Date": "2026-09-20 07:24:35 UTC", "User": "root" }, "Author": "Joan Zhang [aut, cre],\nAileen Johnson [aut],\nChristian P Larsen [cph, aut]", "Maintainer": "Joan Zhang ", "_user": "larsenlab", "_type": "src", "_file": "hlaR_1.0.0.tar.gz", "_fileid": "https://r2.ropensci.org/ccaeb2afbb86e2a5e2e33918159947f81ecfd2656d0dcfe74fcad58e23abecea", "_filesize": 263013, "_sha256": "ccaeb2afbb86e2a5e2e33918159947f81ecfd2656d0dcfe74fcad58e23abecea", "_expires": "2026-12-29T07:28:56.000Z", "_created": "2026-09-20T07:24:35.000Z", "_published": "2026-09-20T07:28:58.604Z", "_jobs": [ { "job": 106041162478, "time": 217, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "10601211400" }, { "job": 106041162376, "time": 198, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "10601381173" 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"success", "_upstream": "https://github.com/larsenlab/hlar", "_commit": { "id": "a7fec958e00d3a7b00f5128900c6b328c2bcb75c", "author": "Joan Zhang <44436425+xzhan50@users.noreply.github.com>", "committer": "GitHub ", "message": "Update README.md", "time": 1677793102 }, "_maintainer": { "name": "Joan Zhang", "email": "joan.zhang@emory.edu", "login": "xzhan50", "description": "", "uuid": 44436425 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "devtools", "role": "Imports" }, { "package": "tidyverse", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "reshape2", "role": "Imports" }, { "package": "schoolmath", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "tidyselect", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "purrr", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "utils", 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"title": "Calculate class I HLA eplet mismatch", "topics": [ "CalEpletMHCI" ] }, { "page": "CalEpletMHCII", "title": "Calculate class II HLA eplet mismatch.", "topics": [ "CalEpletMHCII" ] }, { "page": "CleanAllele", "title": "Clean messy HLA typing data", "topics": [ "CleanAllele" ] }, { "page": "CountAlleleMism", "title": "Count HLA mismatch at the allele level", "topics": [ "CountAlleleMism" ] }, { "page": "EvalAlleleMism", "title": "Evaluate mismatched alleles", "topics": [ "EvalAlleleMism" ] }, { "page": "ImputeHaplo", "title": "Imputation", "topics": [ "ImputeHaplo" ] }, { "page": "utils", "title": "Basic functions", "topics": [ "CalRiskScore", "FuncForCompHaplo", "GenerateLookup", "na_to_empty_string", "utils" ] } ], "_readme": "https://github.com/larsenlab/hlar/raw/HEAD/README.md", "_rundeps": [ "askpass", "backports", "base64enc", "bit", "bit64", "blob", "brew", "brio", "broom", "bslib", "cachem", "callr", "cellranger", "cli", "clipr", "commonmark", "conflicted", "cpp11", 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We have an example cohort that can be loaded into the environment with the following code. This is A cohort of 14 recipients with donor and recipient high resolution HLA typing data for HLA Class I (A, B, C) and HLA Class II (DRB1, DRB3/4/5, and DQb and DQb).", "Step 2: Calculate MHCI mismatch, pull information from result using single and overall outputs.", "Example 1 - MHC-I", "Step 3: Calculate MHCII mismatch and DRDQ risk score, pull information from result using single and overall outputs.", "Step 4: Use visuals to examine the data.", "Sources", "MatchMaker Logic:" ], "created": "2020-10-27 13:59:21", "modified": "2022-10-26 01:46:08", "commits": 25 }, { "source": "allele-haplotype.Rmd", "filename": "allele-haplotype.html", "title": "Imputation", "engine": "knitr::rmarkdown", "headings": [ "Vignette Aims", "Load Test Data Set", "Generate List of Possible Haplotypes and Sort Most likely Pairs", "Impute high-resolution data", "Notes:" ], "created": "2021-01-14 16:03:56", "modified": "2021-10-14 15:20:53", "commits": 13 } ], "_score": 5.296665190261531, "_indexed": true, "_nocasepkg": "hlar", "_universes": [ "larsenlab", "xzhan50" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0.0", "date": "2026-09-20T07:27:57.000Z", "distro": "resolute", "commit": "a7fec958e00d3a7b00f5128900c6b328c2bcb75c", "fileid": "https://r2.ropensci.org/9041e1a4aa6a705fa59f940d2f050eb5d1189ec0b4ab38b50f5f29cca4f67352", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/larsenlab/actions/runs/35496570070" }, { "r": "4.6.1", "os": "linux", "version": "1.0.0", "date": "2026-09-20T07:27:39.000Z", "distro": "resolute", "commit": "a7fec958e00d3a7b00f5128900c6b328c2bcb75c", "fileid": "https://r2.ropensci.org/c196a00fd5ed1fb11d373f20c857c1b35c924b03bc8697f4432b676409b3c791", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/larsenlab/actions/runs/35496570070" }, { "r": "4.5.3", "os": "mac", "version": "1.0.0", "date": "2026-09-20T07:27:22.000Z", "commit": "a7fec958e00d3a7b00f5128900c6b328c2bcb75c", "fileid": "https://r2.ropensci.org/d1e16f5aee717f42e47c1cf34087cfca0868ca2cdd029951ff2f627d2e737eef", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/larsenlab/actions/runs/35496570070" }, { "r": "4.6.1", "os": "mac", "version": "1.0.0", "date": "2026-09-20T07:27:02.000Z", "commit": "a7fec958e00d3a7b00f5128900c6b328c2bcb75c", "fileid": "https://r2.ropensci.org/086afd613e225ab989c21f576fa8645af97aab777d858cfb581a8594a1a94ade", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/larsenlab/actions/runs/35496570070" }, { "r": "4.6.0", "os": "wasm", "version": "1.0.0", "date": "2026-09-20T07:28:20.000Z", "commit": "a7fec958e00d3a7b00f5128900c6b328c2bcb75c", "fileid": "https://r2.ropensci.org/f091bed7961799cdc9f243db809effdb0769abf62049d8cf4541eefd1710fe8b", "status": "success", "buildurl": "https://github.com/r-universe/larsenlab/actions/runs/35496570070" }, { "r": "4.7.0", "os": "win", "version": "1.0.0", "date": "2026-09-20T07:25:52.000Z", "commit": "a7fec958e00d3a7b00f5128900c6b328c2bcb75c", "fileid": "https://r2.ropensci.org/931c9b631bcc75c63fd936c88fea43cf9402c1d73694c29dc7b3758f8300e749", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/larsenlab/actions/runs/35496570070" }, { "r": "4.5.3", "os": "win", "version": "1.0.0", "date": "2026-09-20T07:25:58.000Z", "commit": "a7fec958e00d3a7b00f5128900c6b328c2bcb75c", "fileid": "https://r2.ropensci.org/9a3b80c05f6a3d6eb5b5230bb2d7482ab49c201e33dfb9f62a531e1d9293484c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/larsenlab/actions/runs/35496570070" }, { "r": "4.6.1", "os": "win", "version": "1.0.0", "date": "2026-09-20T07:26:03.000Z", "commit": "a7fec958e00d3a7b00f5128900c6b328c2bcb75c", "fileid": "https://r2.ropensci.org/7e1bfea45557799f31ff1411b6bd4ae3296d53c00923d084cc506f35279e4827", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/larsenlab/actions/runs/35496570070" } ] }