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Processes amino acid alignments produced by the 'IPD-IMGT/HLA (Immuno Polymorphism-ImMunoGeneTics/Human Leukocyte Antigen) Database' to identify user-defined amino acid residue motifs shared across HLA alleles, HLA alleles, or HLA haplotypes, and calculates frequencies based on HLA allele frequency data. 'SSHAARP' (Searching Shared HLA Amino Acid Residue Prevalence) uses 'Generic Mapping Tools (GMT)' software and the 'GMT' R package to generate global frequency heat maps that illustrate the distribution of each user-defined map around the globe. 'SSHAARP' analyzes the allele frequency data described by Solberg et al. (2008) <doi:10.1016/j.humimm.2008.05.001>, a global set of 497 population samples from 185 published datasets, representing 66,800 individuals total. Users may also specify their own datasets, but file conventions must follow the prebundled Solberg dataset, or the mock haplotype dataset.
| Version: | 2.0.5 |
| Depends: | R (≥ 3.6) |
| Imports: | data.table, stringr, gtools, BIGDAWG, gmt, DescTools, dplyr, utils, filesstrings, purrr, stringi, HLAtools |
| Suggests: | knitr, rmarkdown |
| Published: | 2024-12-11 |
| DOI: | 10.32614/CRAN.package.SSHAARP |
| Author: | Livia Tran [aut, cre], Steven Mack [aut], Josh Bredeweg [ctb], Dale Steinhardt [ctb] |
| Maintainer: | Livia Tran <livia.tran at ucsf.edu> |
| License: | GPL (≥ 3) |
| NeedsCompilation: | no |
| SystemRequirements: | GMT (5 or 6), Ghostscript (>=9.6) |
| Materials: | NEWS |
| CRAN checks: | SSHAARP results |
| Reference manual: | SSHAARP.pdf |
| Vignettes: |
SSHAARP Vignette (source, R code) |
| Package source: | SSHAARP_2.0.5.tar.gz |
| Windows binaries: | r-devel: SSHAARP_2.0.5.zip, r-release: SSHAARP_1.1.0.zip, r-oldrel: SSHAARP_2.0.5.zip |
| macOS binaries: | r-release (arm64): SSHAARP_2.0.5.tgz, r-oldrel (arm64): SSHAARP_2.0.5.tgz, r-release (x86_64): SSHAARP_2.0.5.tgz, r-oldrel (x86_64): SSHAARP_2.0.5.tgz |
| Old sources: | SSHAARP archive |
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These binaries (installable software) and packages are in development.
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