RTNsurvival
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see RTNsurvival.
Survival analysis using transcriptional networks inferred by the RTN package
Bioconductor version: 3.9
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("RTNsurvival")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("RTNsurvival")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("RTNsurvival")| RTNsurvival: multivariate survival analysis using transcriptional networks and regulons. | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | GeneRegulation, GeneSetEnrichment, GraphAndNetwork, NetworkEnrichment, NetworkInference, Software, Survival |
| Version | 1.8.3 |
| In Bioconductor since | BioC 3.6 (R-3.4) (6.5 years) |
| License | Artistic-2.0 |
| 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 |
| System Requirements | |
| URL |
See More
| Suggests | Fletcher2013b, knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | RTNsurvival_1.8.3.tar.gz |
| Windows Binary | RTNsurvival_1.8.3.zip |
| Mac OS X 10.11 (El Capitan) | RTNsurvival_1.8.3.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/RTNsurvival |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/RTNsurvival |
| Bioc Package Browser | https://code.bioconductor.org/browse/RTNsurvival/ |
| Package Short Url | https://bioconductor.org/packages/RTNsurvival/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |