ProteoDisco is an R package to facilitate proteogenomics studies.
It houses functions to create customized (variant) protein databases based on user-submitted genomic variants, splice-junctions, fusion genes and manual transcript sequences. The flexible workflow can be adopted to suit a myriad of research and experimental settings.
van de Geer, Wesley S. and van Riet, Job and van de Werken, Harmen J. G. ProteoDisco: a flexible R approach to generate customized protein databases for extended search space of novel and variant proteins in proteogenomic studies. Bioinformatics 2022 38(5), 1437–1439.
The latest development version can be installed directly from GitHub:
# Require/install devtools package if not already installed.
if (!require("devtools")) install.packages("devtools", repos = "http://cran.r-project.org")
# Install ProteoDisco from GitHub.
devtools::install_github(repo = "ErasmusMC-CCBC/ProteoDisco")
library(ProteoDisco)Or from BioConductor:
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ProteoDisco")Please view the vignettes for instructions and tutorials on how to use this package.
browseVignettes("ProteoDisco")