ImmuneSIM: tunable multi-feature simulation of B- and T-cell receptor repertoires for immunoinformatics benchmarking.

ABSTRACT: SUMMARY:B- and T-cell receptor repertoires of the adaptive immune system have become a key target for diagnostics and therapeutics research. Consequently, there is a rapidly growing number of bioinformatics tools for immune repertoire analysis. Benchmarking of such tools is crucial for ensuring reproducible and generalizable computational analyses. Currently, however, it remains challenging to create standardized ground truth immune receptor repertoires for immunoinformatics tool benchmarking. Therefore, we developed immuneSIM, an R package that allows the simulation of native-like and aberrant synthetic full-length variable region immune receptor sequences by tuning the following immune receptor features: (i) species and chain type (BCR, TCR, single and paired), (ii) germline gene usage,

SUBMITTER: Weber CR 

PROVIDER: S-EPMC7334888 | biostudies-literature | 2020 Jun

REPOSITORIES: biostudies-literature