RTNsurvival

This is the development version of RTNsurvival; for the stable release version, see RTNsurvival.

Survival analysis using transcriptional networks inferred by the RTN package

Bioconductor version: Development (3.18)

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>

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

Installation

To install this package, start R (version "4.3") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")

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

Details

biocViews	GeneRegulation, GeneSetEnrichment, GraphAndNetwork, NetworkEnrichment, NetworkInference, Software, Survival
Version	1.25.0
In Bioconductor since	BioC 3.6 (R-3.4) (6 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
Linking To
Suggests	Fletcher2013b, knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics
System Requirements
Enhances
URL

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Build Report

Package Archives

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

Source Package	RTNsurvival_1.25.0.tar.gz
Windows Binary	RTNsurvival_1.25.0.zip
macOS Binary (x86_64)	RTNsurvival_1.25.0.tgz
macOS Binary (arm64)	RTNsurvival_1.25.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/RTNsurvival
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/RTNsurvival
Bioc Package Browser	https://code.bioconductor.org/browse/RTNsurvival/
Package Short Url	https://bioconductor.org/packages/RTNsurvival/
Package Downloads Report	Download Stats