RTNsurvival
This is the released version of RTNsurvival; for the devel version, see RTNsurvival.
Survival analysis using transcriptional networks inferred by the RTN package
Bioconductor version: Release (3.22)
RTNsurvival connects gene regulatory network activity with patient survival. Using regulons inferred by the RTN package, it computes single-sample differential Enrichment Scores (dES) and relates regulon activity patterns to survival outcomes. The package supports both Cox proportional hazards models and Kaplan–Meier analyses, allowing users to identify regulons associated with prognosis and to stratify cohorts based on regulon activity.
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 "4.5") 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 | 1.34.1 |
| In Bioconductor since | BioC 3.6 (R-3.4) (8.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.4.0), RTN(>= 2.32), RTNduals(>= 1.32), methods |
| Imports | survival, RColorBrewer, grDevices, graphics, stats, utils, scales, data.table, egg, ggplot2, pheatmap, dunn.test |
| System Requirements | |
| URL |
See More
| Suggests | 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_1.34.1.tar.gz |
| Windows Binary (x86_64) | RTNsurvival_1.34.0.zip |
| macOS Binary (x86_64) | RTNsurvival_1.34.0.tgz |
| macOS Binary (arm64) | RTNsurvival_1.34.0.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 3.22 | Source Archive |