README.md

In saezlab/CARNIPHAL: tool to run CARNIVAL on phosphoproteomic data

CARNIPHAL

Package for running CARNIVAL with phosphoproteomic data

CARNIPHAL is a method to connect perturbed kinases to deregulated phosphosites downstream. It builds on CARNIVAL, and more specifically the runCARNIVAL wrapper function. As such, it requires the CARNIVAL package (Version 1.3) to be installed. Additionally, it uses OmnipathR to construct a prior knowledge network combining protein-protein and protein-phosphosite interactions. The pipeline requires a vector of input nodes (perturbations/kinases) and measured nodes (phosphosites) and an interactive version of IBM Cplex or CBC-COIN solver as the network optimiser. The IBM ILOG Cplex is freely available through Academic Initiative.

Install

To install CARNIPHAL please run:

devtools::install_github('saezlab/CARNIPHAL')

saezlab/CARNIPHAL documentation built on Dec. 22, 2021, 9:12 p.m.