Package: RTNsurvival
Type: Package
Title: Survival analysis using transcriptional networks inferred by the
        RTN package
Version: 1.12.0
Author: Clarice S. Groeneveld, Vinicius S. Chagas, Mauro A. A. Castro
Maintainer: Clarice Groeneveld <clari.groeneveld@gmail.com>, Mauro A. A. Castro <mauro.a.castro@gmail.com>
Depends: R(>= 3.5), RTN(>= 2.6.3), RTNduals(>= 1.6.1), methods
Imports: survival, RColorBrewer, grDevices, graphics, stats, utils,
        scales, data.table, egg, ggplot2, pheatmap, dunn.test
Suggests: Fletcher2013b, knitr, rmarkdown, BiocStyle, RUnit,
        BiocGenerics
Description: 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.
License: Artistic-2.0
biocViews: NetworkEnrichment, Survival, GeneRegulation,
        GeneSetEnrichment, NetworkInference, GraphAndNetwork
LazyData: TRUE
VignetteBuilder: knitr
Encoding: UTF-8
RoxygenNote: 7.0.2
git_url: https://git.bioconductor.org/packages/RTNsurvival
git_branch: RELEASE_3_11
git_last_commit: aa7aa13
git_last_commit_date: 2020-04-27
Date/Publication: 2020-04-27
NeedsCompilation: no
Packaged: 2020-04-28 03:04:50 UTC; biocbuild
Built: R 4.0.0; ; 2020-05-10 15:57:57 UTC; unix
