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Survival analysis using transcriptional networks inferred by the RTN package

Bioconductor version: Release (3.19)

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>, Mauro A. A. Castro <mauro.a.castro at>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


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


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

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


biocViews GeneRegulation, GeneSetEnrichment, GraphAndNetwork, NetworkEnrichment, NetworkInference, Software, Survival
Version 1.28.0
In Bioconductor since BioC 3.6 (R-3.4) (6.5 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
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Suggests Fletcher2013b, knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics
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Follow Installation instructions to use this package in your R session.

Source Package RTNsurvival_1.28.0.tar.gz
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macOS Binary (x86_64) RTNsurvival_1.28.0.tgz
macOS Binary (arm64) RTNsurvival_1.28.0.tgz
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