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

ABSTRACT: 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. ProteoDisco (R package version ≥ 1.0.0) is available on Bioconductor at https://doi.org/doi:10.18129/B9.bioc.ProteoDisco and from https://github.com/ErasmusMC-CCBC/ProteoDisco/. Supplementary table, figures and data files are available at Bioinformatics online.

SUBMITTER: van de Geer WS 

PROVIDER: S-EPMC8826347 | biostudies-literature | 2021 Dec

REPOSITORIES: biostudies-literature