visProteomics

visProteomics helps with the exploration and visualization of proteomics data obtained with the process of fractionation. Fractionation of samples is often used in proteomics to improve signal-to-noise ratio and proteome coverage. visProteomics explores attributes of proteins detected in different fractions through both graphical and tabular representation.

Venn/Euler diagrams are widely used for data summarization and there are many plotting tools available. visProteomics defines a complementary tabular function. The resulting data frame summarizes attributes of elements found in different regions of the Venn diagram. This generic function can be used for any data set.

visProteomics package as part of proteomics analysis

Installation

devtools::install_github("ivabudimir/visProteomics")

For installation of vignettes together with the package, add “build_vignettes=TRUE”.

Usage

library(visProteomics)

For the exploration and visualization of a fractionated proteomic sample, read vignette vis-fractions. If you need help with the data preparation because the software for protein identification returned a separate list of proteins for each fraction, first read vignette merge-fractions.

For the tabular description od the Venn diagram regions, read vignette explore-venn.

License

visProteomics is open source software, licensed under GPL-3.