ProteoDisco: a flexible R approach to generate customized protein databases for extended search space of novel and
Wesley S van de Geer1,2,3, Job van Riet1,2,3, Harmen J G van de Werken1,3,4
1Cancer Computational Biology Center, Erasmus MC Cancer Institute, University Medical Center, 3015 GD Rotterdam, The Netherlands.
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/doi:10.18129/B9.bioc.ProteoDisco and from https://github.com/ErasmusMC-CCBC/ProteoDisco/.
Supplementary Information:
Supplementary data are available at Bioinformatics online.
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