RTNsurvival
This is the development version of RTNsurvival; for the stable release version, see RTNsurvival.
Survival analysis using transcriptional networks inferred by the RTN package
Bioconductor version: Development (3.24)
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.
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
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 | 1.37.0 |
| In Bioconductor since | BioC 3.6 (R-3.4) (9 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_1.37.0.tar.gz |
| Windows Binary (x86_64) | RTNsurvival_1.37.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | RTNsurvival_1.37.0.tgz |
| macOS Binary (sonoma-arm64) | RTNsurvival_1.37.0.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 |