Package: SSHAARP 1.1.0

Livia Tran

SSHAARP: Searching Shared HLA Amino Acid Residue Prevalence

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, and calculates the frequencies of those motifs 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.

Authors:Livia Tran [aut, cre], Steven Mack [aut], Josh Bredeweg [ctb], Dale Steinhardt [ctb]

SSHAARP_1.1.0.tar.gz
SSHAARP_1.1.0.tar.gz(r-4.5-noble)SSHAARP_1.1.0.tar.gz(r-4.4-noble)
SSHAARP_1.1.0.tgz(r-4.4-emscripten)SSHAARP_1.1.0.tgz(r-4.3-emscripten)
SSHAARP.pdf |SSHAARP.html✨
SSHAARP/json (API)
NEWS

# Install 'SSHAARP' in R:
install.packages('SSHAARP', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • AA_atlas - Exon boundaries for all exons in protein coding genes in the IPD-IMGT/HLA Database release v 3.39.0
  • IMGTprotalignments - Protein alignments for all protein coding genes in the IPD-IMGT/HLA Database release v 3.39.0.
  • solberg_dataset - Solberg Dataset

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.00 score 210 downloads 5 exports 113 dependencies

Last updated 3 years agofrom:d8da36469e. Checks:OK: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 08 2024
R-4.5-linuxOKNov 08 2024

Exports:BLAASDcheckMotifdataSubsetfindMotifPALM

Dependencies:arsenalaskpassbackportsbase64encBIGDAWGbootbslibcachemcellrangercheckmateclasscliclustercodetoolscolorspacecpp11crayoncurldata.tableDescToolsdigestdplyre1071evaluateExactexpmfansifarverfastmapfilesstringsfontawesomeforeignFormulafsgenericsggplot2gldgluegmtgridExtragtablegtoolshaplo.statshighrHmischmshtmlTablehtmltoolshtmlwidgetshttrisobandjquerylibjsonliteknitrlabelinglatticelifecyclelmommagrittrMASSMatrixMatrixModelsmemoisemgcvmimemultcompmunsellmvtnormnlmennetopensslpillarpkgconfigpolsplineprettyunitsprogressproxypurrrquantregR6rappdirsRColorBrewerRcppreadxlrematchrlangrmarkdownrmsrootSolverpartrstudioapisandwichsassscalesSparseMstrexstringistringrsurvivalsysTH.datatibbletidyselecttinytexutf8vctrsviridisviridisLitewithrxfunXMLyamlzoo

SSHAARP: Searching Shared HLA Amino Acid Residue Prevalence

Livia Tran - [email protected]

Rendered fromvignette.Rmdusingknitr::rmarkdownon Nov 08 2024.

Last update: 2021-09-17
Started: 2020-04-27