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.
| Version: | 1.0.0 |
| Depends: | R (≥ 4.1.0) |
| Imports: | devtools,tidyverse,dplyr,reshape2,schoolmath,tibble,tidyselect,stringr,purrr,tidyr, utils,readr,janitor |
| Suggests: | knitr,rmarkdown |
| Published: | 2023-01-31 |
| DOI: | 10.32614/CRAN.package.hlaR |
| Author: | Joan Zhang [aut, cre], Aileen Johnson [aut], Christian P Larsen [cph, aut] |
| Maintainer: | Joan Zhang <joan.zhang at emory.edu> |
| BugReports: | https://github.com/LarsenLab/hlaR/issues |
| License: | MIT + fileLICENSE |
| URL: | https://pubmed.ncbi.nlm.nih.gov/35101308/,https://emory-larsenlab.shinyapps.io/hlar_shiny/ |
| NeedsCompilation: | no |
| CRAN checks: | hlaR results |
| Reference manual: | hlaR.html ,hlaR.pdf |
| Vignettes: | Imputation (source,R code) Eplet Mismatch (source,R code) |
| Package source: | hlaR_1.0.0.tar.gz |
| Windows binaries: | r-devel:hlaR_1.0.0.zip, r-release:hlaR_1.0.0.zip, r-oldrel:hlaR_1.0.0.zip |
| macOS binaries: | r-release (arm64):hlaR_1.0.0.tgz, r-oldrel (arm64):hlaR_1.0.0.tgz, r-release (x86_64):hlaR_1.0.0.tgz, r-oldrel (x86_64):hlaR_1.0.0.tgz |
| Old sources: | hlaR archive |
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