Package: hlaR 1.0.0
Joan Zhang
hlaR: Tools for HLA Data
A streamlined tool for eplet analysis of donor and recipient HLA (human leukocyte antigen) mismatch. Messy, low-resolution HLA typing data is cleaned, and imputed to high-resolution using the NMDP (National Marrow Donor Program) haplotype reference database <https://haplostats.org/haplostats>. High resolution data is analyzed for overall or single antigen eplet mismatch using a reference table (currently supporting 'HLAMatchMaker' <http://www.epitopes.net> versions 2 and 3). Data can enter or exit the workflow at different points depending on the user's aims and initial data quality.
Authors:
hlaR_1.0.0.tar.gz
hlaR_1.0.0.zip(r-4.5)hlaR_1.0.0.zip(r-4.4)hlaR_1.0.0.zip(r-4.3)
hlaR_1.0.0.tgz(r-4.4-any)hlaR_1.0.0.tgz(r-4.3-any)
hlaR_1.0.0.tar.gz(r-4.5-noble)hlaR_1.0.0.tar.gz(r-4.4-noble)
hlaR_1.0.0.tgz(r-4.4-emscripten)hlaR_1.0.0.tgz(r-4.3-emscripten)
hlaR.pdf |hlaR.html✨
hlaR/json (API)
| # Install 'hlaR' in R: |
| install.packages('hlaR', repos = c('https://larsenlab.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/larsenlab/hlar/issues
Last updated 2 years agofrom:a7fec958e0. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 12 2024 |
| R-4.5-win | OK | Nov 12 2024 |
| R-4.5-linux | OK | Nov 12 2024 |
| R-4.4-win | OK | Nov 12 2024 |
| R-4.4-mac | OK | Nov 12 2024 |
| R-4.3-win | OK | Nov 12 2024 |
| R-4.3-mac | OK | Nov 12 2024 |
Exports:CalAlleleMismFreqCalAlleleTopNCalEpletMHCICalEpletMHCIICleanAlleleCountAlleleMismEvalAlleleMismImputeHaplo
Dependencies:askpassbackportsbase64encbitbit64blobbrewbriobroombslibcachemcallrcellrangerclicliprcolorspacecommonmarkconflictedcpp11crayoncredentialscurldata.tableDBIdbplyrdescdevtoolsdiffobjdigestdownlitdplyrdtplyrellipsisevaluatefansifarverfastmapfontawesomeforcatsfsgarglegenericsgertggplot2ghgitcredsgluegoogledrivegooglesheets4gtablehavenhighrhmshtmltoolshtmlwidgetshttpuvhttrhttr2idsiniisobandjanitorjquerylibjsonliteknitrlabelinglaterlatticelifecyclelubridatemagrittrMASSMatrixmemoisemgcvmimeminiUImodelrmunsellnlmeopensslpillarpkgbuildpkgconfigpkgdownpkgloadplyrpraiseprettyunitsprocessxprofvisprogresspromisespspurrrR6raggrappdirsrcmdcheckRColorBrewerRcppreadrreadxlrematchrematch2remotesreprexreshape2rlangrmarkdownroxygen2rprojrootrstudioapirversionsrvestsassscalesschoolmathselectrsessioninfoshinysnakecasesourcetoolsstringistringrsyssystemfontstestthattextshapingtibbletidyrtidyselecttidyversetimechangetinytextzdburlcheckerusethisutf8uuidvctrsviridisLitevroomwaldowhiskerwithrxfunxml2xopenxtableyamlzip
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Evaluate the frequency of specific allele mismatches | CalAlleleMismFreq |
| topN most frequent HLA alleles | CalAlleleTopN |
| Calculate class I HLA eplet mismatch | CalEpletMHCI |
| Calculate class II HLA eplet mismatch. | CalEpletMHCII |
| Clean messy HLA typing data | CleanAllele |
| Count HLA mismatch at the allele level | CountAlleleMism |
| Evaluate mismatched alleles | EvalAlleleMism |
| Imputation | ImputeHaplo |
| Basic functions | CalRiskScore FuncForCompHaplo GenerateLookup na_to_empty_string utils |
