PrInCE: an R/Bioconductor package for protein-protein interaction network inference from co-fractionation mass spectrometry data.

ABSTRACT

SUMMARY: We present PrInCE, an R/Bioconductor package that employs a machine-learning approach to infer protein-protein interaction networks from co-fractionation mass spectrometry (CF-MS) data. Previously distributed as a collection of Matlab scripts, our ground-up rewrite of this software package in an open-source language dramatically improves runtime and memory requirements. We describe several new features in the R implementation, including a test for the detection of co-eluting protein complexes and a method for differential network analysis. PrInCE is extensively documented and fully compatible with Bioconductor classes, ensuring it can fit seamlessly into existing proteomics workflows. AVAILABILITY AND IMPLEMENTATION PrInCE is available from Bioconductor (https//www.bioconductor.org/packages/devel/bioc/html/PrInCE.html). Source code is freely available from GitHub under the MIT license (https//github.com/fosterlab/PrInCE). Support is provided via the GitHub issues tracker (https//github.com/fosterlab/PrInCE/issues). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.