The bppg package contains functionality to create and characterize bipartite graphs that model the relationship between peptides and proteins in bottom-up proteomics. With these graphs, protein ratios (fold change between two sample groups) are calculated from the respective measured peptide ratios. The main aim is to make use of quantitative information contained in shared peptides and making it possible to quantify proteins without shared peptides.
The current release version can be installed from Bioconductor usin the following code:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("bppg")You can also install the development version of bppg from GitHub with:
# install.packages("pak")
pak::pak("mpc-bioinformatics/bppg")For details on the usage of bppg please see the vignette.
The quantification algorithm in bppg is build on the PhD thesis
"Improvement of protein quantification for proteins with shared peptides by using bipartite peptide-protein graphs"
http://dx.doi.org/10.17877/DE290R-25361
The development of bppg is funded by the German Research Foundation (DFG, project number 532401634), the German Network for Bioinformatics Infrastructure (de.NBI & ELIXIR-DE, Federal Ministry of Research, Technology and Space, grant number W-de.NBI-005) and the Core Unit for Bioinformatics of the Medical Faculty of the Ruhr University Bochum (CUBiMed.RUB).