KinSwingR: KinSwingR: A package for predicting kinase activity

In awaardenberg/KinSwingR: KinSwingR: network-based kinase activity prediction

Description

This package provides functionality for kinase-subtrate prediction, and integration with phosphopeptide fold change and signficance to assess the local connectivity (swing) of kinase-substrate networks. The final output of KinSwingR is a score that is normalised and weighted for prediction of kinase activity.

Details

Contact [e-mail] for questions relating to functionality.

buildPWM function

Builds PWMs for kinases from a table of kinases and known substrate sequences.

scoreSequences function

Score kinase PWMs matches against a set of peptide seqeuences.

swing function

Integrates kinase PWMs matches against peptide seqeuences and directionality as well as significance of peptides for prediction of kinase activity.

cleanAnnotation function

Function for extracting peptides from multimapped data

awaardenberg/KinSwingR documentation built on May 9, 2019, 8:12 a.m.