{ "_id": "6a114648acfb0bcc41ce7953", "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": "2026-05-23 06:13:03 UTC", "User": "root" }, "Author": "Joan Zhang [aut, cre],\nAileen Johnson [aut],\nChristian P Larsen [cph, aut]", "Maintainer": "Joan Zhang ", "MD5sum": "0e5feeeb85160a3094d69f710272fa03", "_user": "larsenlab", "_type": "src", "_file": "hlaR_1.0.0.tar.gz", "_fileid": "a918f987bba676fd34d202e51986b326f0c3208698b721b3229da3f0173c6055", "_filesize": 261876, "_sha256": "a918f987bba676fd34d202e51986b326f0c3208698b721b3229da3f0173c6055", "_created": "2026-05-23T06:13:03.000Z", "_published": "2026-05-23T06:16:40.844Z", "_distro": "noble", "_jobs": [ { "job": 77502354841, "time": 185, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7174852780" }, { "job": 77502354824, "time": 175, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7174852056" 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"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 }, "_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", "role": "Imports" }, { "package": "readr", "role": "Imports" }, { "package": "janitor", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "larsenlab", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 9, "_contributors": [ { "user": "xzhan50", "count": 488, "uuid": 44436425 }, { "user": "clarsenemory", "count": 16, "uuid": 28197980 }, { "user": "aileencj", "count": 5, "uuid": 68113683 } ], "_userbio": { "uuid": 37153938, "type": "organization", "name": "LarsenLab", "description": "integrating clinical data science and systems biology for better health" }, "_downloads": { "count": 256, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/hlaR" }, "_devurl": "https://github.com/larsenlab/hlar", "_searchresults": 9, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/hlaR.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/larsenlab/hlar", "_realowner": "larsenlab", "_cranurl": true, "_releases": [ { "version": "0.1.0", "date": "2021-04-13" }, { "version": "0.1.1", "date": "2021-09-27" }, { "version": "0.1.2", "date": "2022-02-01" }, { "version": "0.1.3", "date": "2022-05-14" }, { "version": "0.1.4", "date": "2022-09-12" }, { "version": "0.1.5", "date": "2022-10-24" }, { "version": "0.1.6", "date": "2022-12-21" }, { "version": "1.0.0", "date": "2023-01-31" } ], "_exports": [ "CalAlleleMismFreq", "CalAlleleTopN", "CalEpletMHCI", "CalEpletMHCII", "CleanAllele", "CountAlleleMism", "EvalAlleleMism", "ImputeHaplo" ], "_help": [ { "page": "CalAlleleMismFreq", "title": "Evaluate the frequency of specific allele mismatches", "topics": [ "CalAlleleMismFreq" ] }, { "page": "CalAlleleTopN", "title": "topN most frequent HLA alleles", "topics": [ "CalAlleleTopN" ] }, { "page": "CalEpletMHCI", "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", "crayon", "credentials", "curl", "data.table", "DBI", "dbplyr", "desc", 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"stringi", "stringr", "sys", "systemfonts", "testthat", "textshaping", "tibble", "tidyr", "tidyselect", "tidyverse", "timechange", "tinytex", "tzdb", "urlchecker", "usethis", "utf8", "uuid", "vctrs", "viridisLite", "vroom", "waldo", "whisker", "withr", "xfun", "xml2", "xopen", "xtable", "yaml", "zip" ], "_vignettes": [ { "source": "eplet-mm.Rmd", "filename": "eplet-mm.html", "title": "Eplet Mismatch", "engine": "knitr::rmarkdown", "headings": [ "Aims", "Overview", "Use Cases:", "Example: Investigate the Importance of Eplet Mismatch in Retrospective Transplant Cohort", "Step 1: Import recipient and donor typing data. 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": 5.2552725051033065, "_indexed": true, "_nocasepkg": "hlar", "_universes": [ "larsenlab", "xzhan50" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0.0", "date": "2026-05-23T06:15:51.000Z", "distro": "noble", "commit": "a7fec958e00d3a7b00f5128900c6b328c2bcb75c", "fileid": "51591674cf43b1b9f4b25f1446b9ee1eec81a19ddbb84106336738412d5b1ae8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/larsenlab/actions/runs/26325400139" }, { "r": "4.6.0", "os": "linux", "version": "1.0.0", "date": "2026-05-23T06:15:47.000Z", "distro": "noble", "commit": "a7fec958e00d3a7b00f5128900c6b328c2bcb75c", "fileid": "5be8247a923533cc08b37311a24c0bb947b128e8799600ab7ed8420af327022c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/larsenlab/actions/runs/26325400139" }, { "r": "4.5.3", "os": "mac", "version": "1.0.0", "date": "2026-05-23T06:15:22.000Z", "commit": "a7fec958e00d3a7b00f5128900c6b328c2bcb75c", "fileid": "949edd12142cb1029fb60ce3dbd4a52698a60808a941e5b93db6c045b208dd84", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/larsenlab/actions/runs/26325400139" }, { "r": "4.6.0", "os": "mac", "version": "1.0.0", "date": "2026-05-23T06:14:56.000Z", "commit": "a7fec958e00d3a7b00f5128900c6b328c2bcb75c", "fileid": "94b7c3857e9dbfa7eb25a529276902e6c3f16c518fd000a5b31f1ee63bca841f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/larsenlab/actions/runs/26325400139" }, { "r": "4.6.0", "os": "wasm", "version": "1.0.0", "date": "2026-05-23T06:15:44.000Z", "commit": "a7fec958e00d3a7b00f5128900c6b328c2bcb75c", "fileid": "76e316a4e5d738b9a45c532cde3ef9a36c86131daba5bb40e63ade9a9fb9e4ff", "status": "success", "buildurl": "https://github.com/r-universe/larsenlab/actions/runs/26325400139" }, { "r": "4.7.0", "os": "win", "version": "1.0.0", "date": "2026-05-23T06:14:37.000Z", "commit": "a7fec958e00d3a7b00f5128900c6b328c2bcb75c", "fileid": "68db75683c3ce909f79a470f81f3d9812c32bafeb92fb424befc6434aecffb13", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/larsenlab/actions/runs/26325400139" }, { "r": "4.5.3", "os": "win", "version": "1.0.0", "date": "2026-05-23T06:14:22.000Z", "commit": "a7fec958e00d3a7b00f5128900c6b328c2bcb75c", "fileid": "8bb6d7ce43b8c0c0286b0ee05dd160cf038c028269a3a35fbb2ef446ee30e9b0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/larsenlab/actions/runs/26325400139" }, { "r": "4.6.0", "os": "win", "version": "1.0.0", "date": "2026-05-23T06:14:22.000Z", "commit": "a7fec958e00d3a7b00f5128900c6b328c2bcb75c", "fileid": "5ae7083009ba3f62915a07134c95737913d4681e22bb806d3c976f4d685410a8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/larsenlab/actions/runs/26325400139" } ] }