DOI: 10.18129/B9.bioc.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 (3.7)

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")):


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HTML R Script RTNsurvival: multivariate survival analysis using transcriptional networks and regulons.
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biocViews GeneRegulation, GeneSetEnrichment, GraphAndNetwork, NetworkEnrichment, NetworkInference, Software, Survival
Version 1.3.4
License Artistic-2.0
Depends R (>= 3.3.3), methods, RTN
Imports survival, RColorBrewer, grDevices, graphics, stats, RTNduals, png, utils
Suggests Fletcher2013b, pheatmap, knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics
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Imports Me
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Source Package RTNsurvival_1.3.4.tar.gz
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Source Repository git clone https://git.bioconductor.org/packages/RTNsurvival
Package Short Url http://bioconductor.org/packages/RTNsurvival/
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