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DOI: 10.18129/B9.bioc.RTNsurvival    

This is the development version of RTNsurvival; to use it, please install the devel version of Bioconductor.

Survival analysis using transcriptional networks inferred by the RTN package

Bioconductor version: Development (3.6)

RTNsurvival is a tool for integrating regulons generated by the RTN package with survival information for the same set of samples (i.e. a cohort). It visualizes the integrated data using 2-tailed Gene Set Enrichment Analysis (GSEA2) approach and survival plots [@Castro2016]. This package is implemented using S4 classes and methods for plots and analyses. There are two main survival analyses generated by RTNsurvival: a Cox Proportional Hazards approach used to model regulons as predictors of survival time, and a Kaplan-Meier analysis showing the stratification of a cohort based on the regulon activity. 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. The 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")):


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HTML R Script RTNsurvival: An R/Bioconductor package for survival analysis using transcriptional networks and regulons.
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biocViews GeneRegulation, GeneSetEnrichment, GraphAndNetwork, NetworkEnrichment, NetworkInference, Software, Survival
Version 0.99.13
In Bioconductor since BioC 3.6 (R-3.4)
License Artistic-2.0
Depends R (>= 3.4), methods, RTN
Imports survival, RColorBrewer, grDevices, graphics, stats
Suggests Fletcher2013b, pheatmap, knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics
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