ProteoDisco: a flexible R approach to generate customized protein databases for extended search space of novel and variant proteins in proteogenomic studies.

ABSTRACT

SUMMARY: We present an R-based open-source software termed ProteoDisco that allows for flexible incorporation of genomic variants, fusion genes and (aberrant) transcriptomic variants from standardized formats into protein variant sequences. ProteoDisco allows for a flexible step-by-step workflow allowing for in-depth customization to suit a myriad of research approaches in the field of proteogenomics, on all organisms for which a reference genome and transcript annotations are available. AVAILABILITY AND IMPLEMENTATION ProteoDisco (R package version ≥ 1.0.0) is available on Bioconductor at https//doi.org/doi10.18129/B9.bioc.ProteoDisco and from https//github.com/ErasmusMC-CCBC/ProteoDisco/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.