RTNsurvival

DOI: 10.18129/B9.bioc.RTNsurvival    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see RTNsurvival.

Survival analysis using transcriptional networks inferred by the RTN package

Bioconductor version: 3.13

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.

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>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("RTNsurvival")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("RTNsurvival")

 

HTML	R Script	RTNsurvival: multivariate survival analysis using transcriptional networks and regulons.
PDF		Reference Manual
Text		NEWS

Details

biocViews	GeneRegulation, GeneSetEnrichment, GraphAndNetwork, NetworkEnrichment, NetworkInference, Software, Survival
Version	1.16.0
In Bioconductor since	BioC 3.6 (R-3.4) (4 years)
License	Artistic-2.0
Depends	R (>= 3.6.3), RTN(>= 2.14.1), RTNduals(>= 1.14.1), methods
Imports	survival, RColorBrewer, grDevices, graphics, stats, utils, scales, data.table, egg, ggplot2, pheatmap, dunn.test
LinkingTo
Suggests	Fletcher2013b, knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics
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Package Archives

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

Source Package	RTNsurvival_1.16.0.tar.gz
Windows Binary	RTNsurvival_1.16.0.zip
macOS 10.13 (High Sierra)	RTNsurvival_1.16.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/RTNsurvival
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/RTNsurvival
Package Short Url	https://bioconductor.org/packages/RTNsurvival/
Package Downloads Report	Download Stats