csgroen/RTNsurvival: Survival analysis using transcriptional networks inferred by the RTN package

RTNsurvival is a tool for integrating regulons generated by the RTN package with survival information. For a given regulon, the 2-tailed GSEA approach computes a differential Enrichment Score (dES) for each individual sample, and the dES distribution of all samples is then used to assess the survival statistics for the cohort. There are two main survival analysis workflows: a Cox Proportional Hazards approach used to model regulons as predictors of survival time, and a Kaplan-Meier analysis assessing the stratification of a cohort based on the regulon activity. All plots can be fine-tuned to the user's specifications.

Getting started

Package details

AuthorClarice S. Groeneveld, Vinicius S. Chagas, Mauro A. A. Castro
Bioconductor views GeneRegulation GeneSetEnrichment GraphAndNetwork NetworkEnrichment NetworkInference Survival
MaintainerClarice Groeneveld <[email protected]>, Mauro A. A. Castro <[email protected]>
LicenseArtistic-2.0
Version1.7.3
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
install.packages("devtools")
library(devtools)
install_github("csgroen/RTNsurvival")
csgroen/RTNsurvival documentation built on April 2, 2019, 9:56 p.m.