selective Cross Reactive Antigen Presentation (command line version)
Commandline version of sCRAP
https://marisshiny.research.chop.edu/sCRAP/
Please cite this article:
Yarmarkovich, M., Marshall, Q.F., Warrington, J.M. et al. Cross-HLA targeting of intracellular oncoproteins with peptide-centric CARs. Nature (2021). https://doi.org/10.1038/s41586-021-04061-6
Clone or download the entire repository. Executed the application with R on unix/linux.
Usage: Rscript sCRAP.R -p <peptide> -l <HLA-allele> {arguments}
Options:
-p PEPTIDE, --peptide=PEPTIDE
(Required) peptide query - {character}
-l HLA, --hla=HLA
(Required) hla allele in format: HLA-{allele}, eg.'HLA-A0201' 'HLA-A0301'
-s HOTSPOTS, --hotspots=HOTSPOTS
hotspots locations, numeric value 1-9 seperated by commas
-o OUTDIR, --outdir=OUTDIR
Output directory name
-f FILENAME, --filename=FILENAME
Output file basename
-d DATADIR, --datadir=DATADIR
data directory
-m HLADIR, --hladir=HLADIR
hla data directory
-t FILETYPE, --filetype=FILETYPE
select output file format (csv/tsv)
-h, --help
Show this help message and exit