The CCs4prot package allows to build a graph from shotgun proteomic identifications and calculate its connected components.
The CCs4prot package implements a transcriptome-informed filtering strategy to reduce ambiguity of protein identifications and allows to measure the impact of the filtering on ambiguity by assessment of the proportion and size of multi-protein CCs and by visual inspection of peptide-to-protein mappings for ambiguous identifications.
Download the package with the git clone command:
git clone https://github.com/laurafancello/CCs4prot.git
Initiate R and install the R package using devtools (devtools needs to be installed as well)
library("devtools")
devtools::install("CCs4prot")
To learn how to use CCs4prot, please refer to the introductory vignette posted at this link:
Distributed under the GPL-3 License.
Laura Fancello - laura.fancello@cea.fr
Thomas.Burger - thomas.burger@cea.fr