To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("RTNsurvival")

In most cases, you don't need to download the package archive at all.

RTNsurvival

DOI: 10.18129/B9.bioc.RTNsurvival    

This is the development version of RTNsurvival; to use it, please install the devel version of Bioconductor.

Survival analysis using transcriptional networks inferred by the RTN package

Bioconductor version: Development (3.6)

RTNsurvival is a tool for integrating regulons generated by the RTN package with survival information for the same set of samples (i.e. a cohort). It visualizes the integrated data using 2-tailed Gene Set Enrichment Analysis (GSEA2) approach and survival plots [@Castro2016]. This package is implemented using S4 classes and methods for plots and analyses. There are two main survival analyses generated by RTNsurvival: a Cox Proportional Hazards approach used to model regulons as predictors of survival time, and a Kaplan-Meier analysis showing the stratification of a cohort based on the regulon activity. 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. The plots can be fine-tuned to the user's specifications.

Author: Clarice S. Groeneveld, Vinicius S. Chagas, Mauro A. A. Castro

Maintainer: Clarice Groeneveld <clari.groeneveld at gmail.com>, Mauro A. A. Castro <mauro.a.castro at gmail.com>

Citation (from within R, enter citation("RTNsurvival")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("RTNsurvival")

Documentation

HTML R Script RTNsurvival: An R/Bioconductor package for survival analysis using transcriptional networks and regulons.
PDF   Reference Manual
Text   NEWS

Details

biocViews GeneRegulation, GeneSetEnrichment, GraphAndNetwork, NetworkEnrichment, NetworkInference, Software, Survival
Version 0.99.13
In Bioconductor since BioC 3.6 (R-3.4)
License Artistic-2.0
Depends R (>= 3.4), methods, RTN
Imports survival, RColorBrewer, grDevices, graphics, stats
LinkingTo
Suggests Fletcher2013b, pheatmap, knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source RTNsurvival_0.99.13.tar.gz
Windows Binary RTNsurvival_0.99.13.zip
Mac OS X 10.11 (El Capitan) RTNsurvival_0.99.13.tgz
Source Repository git clone https://git.bioconductor.org/packages/RTNsurvival
Package Short Url http://bioconductor.org/packages/RTNsurvival/
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