RTNsurvival
Survival analysis using transcriptional networks inferred by the RTN package
Bioconductor version: 3.23 · Package version: 1.36.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
RTNsurvival integrates regulons inferred by the RTN package with survival data. For each regulon, a two-tailed GSEA framework computes a differential Enrichment Score (dES) at the individual-sample level. The resulting dES distribution across samples is then used to evaluate survival associations within the cohort. Two primary workflows are supported: (i) Cox proportional hazards models, in which regulon activities are treated as predictors of survival time, and (ii) Kaplan–Meier analyses assessing cohort stratification based on regulon activity. All graphical outputs are customizable according to user specifications.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("RTNsurvival")Details
| Maintainer | Clarice Groeneveld <clari.groeneveld@gmail.com>, Mauro A. A. Castro <mauro.a.castro@gmail.com> |
| Author | Clarice S. Groeneveld, Vinicius S. Chagas, Mauro A. A. Castro |
| License | Artistic-2.0 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | GeneRegulation, GeneSetEnrichment, GraphAndNetwork, NetworkEnrichment, NetworkInference, Software, Survival |
| Package Short Url | https://bioconductor.org/packages/RTNsurvival/ |
Citation
From within R, enter citation("RTNsurvival"):
Clarice S. Groeneveld, Vinicius S. Chagas, Mauro A. A. Castro. RTNsurvival: Survival analysis using transcriptional networks inferred by the RTN package. doi:10.18129/B9.bioc.RTNsurvival, R package version 1.36.0, https://bioconductor.org/packages/RTNsurvival.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | RTNsurvival_1.36.0.tar.gz |
| Windows binary (x86_64) | RTNsurvival_1.36.0.zip |
| macOS binary (arm64) | RTNsurvival_1.36.0.tgz |
| macOS binary (x86_64) | RTNsurvival_1.36.0.tgz |
Dependencies
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
Suggests: knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics