DOI: 10.18129/B9.bioc.RTNsurvival    

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see RTNsurvival.

Survival analysis using transcriptional networks inferred by the RTN package

Bioconductor version: 3.7

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>

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biocViews GeneRegulation, GeneSetEnrichment, GraphAndNetwork, NetworkEnrichment, NetworkInference, Software, Survival
Version 1.4.5
License Artistic-2.0
Depends R (>= 3.5), RTN(>= 2.4.5), RTNduals(>= 1.4.4), methods
Imports survival, RColorBrewer, grDevices, graphics, stats, utils, scales
Suggests Fletcher2013b, pheatmap, knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics
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