Package: RTNsurvival 1.37.0

Clarice Groeneveld

RTNsurvival: Survival analysis using transcriptional networks inferred by the RTN package

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.

Authors:Clarice S. Groeneveld, Vinicius S. Chagas, Mauro A. A. Castro

RTNsurvival_1.37.0.tar.gz
RTNsurvival_1.37.0.zip(r-4.7)RTNsurvival_1.37.0.zip(r-4.6)RTNsurvival_1.37.0.zip(r-4.5)
RTNsurvival_1.37.0.tgz(r-4.6-any)RTNsurvival_1.37.0.tgz(r-4.5-any)
RTNsurvival_1.37.0.tar.gz(r-4.7-any)RTNsurvival_1.37.0.tar.gz(r-4.6-any)
RTNsurvival_1.37.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
RTNsurvival/json (API)

# Install 'RTNsurvival' in R:

install.packages('RTNsurvival', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

survival.data - A pre-processed dataset for demonstration purposes only.

On BioConductor:RTNsurvival-1.37.0(bioc 3.24)RTNsurvival-1.36.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

networkenrichment survival generegulation genesetenrichment networkinference graphandnetwork

3.78 score 15 scripts 1 mentions 20 exports 153 dependencies

Last updated from:0723cd1b71. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	209
linux-devel-x86_64	NOTE	366
source / vignettes	OK	274
linux-release-x86_64	NOTE	337
macos-release-arm64	NOTE	239
macos-oldrel-arm64	NOTE	208
windows-devel	NOTE	257
windows-release	NOTE	259
windows-oldrel	NOTE	256
wasm-release	OK	155

Exports:hclust_semisupervised tni2tnsPreprocess tnsAREA3 tnsCox tnsCoxInteraction tnsGet tnsGSEA2 tnsInteraction tnsKM tnsKmInteraction tnsPlotCovariates tnsPlotCox tnsPlotCoxInteraction tnsPlotGSEA2 tnsPlotKM tnsPlotKmInteraction tnsPlotSRE tnsSRD tnsSRE tnsStratification

Dependencies:abind askpass backports base64enc Biobase BiocGenerics boot broom bslib ca cachem car carData class cli cluster codetools colorspace corrr cowplot cpp11 crosstalk curl data.table DelayedArray Deriv digest doBy dplyr dunn.test e1071 egg evaluate farver fastmap fontawesome foreach forecast Formula fracdiff fs gclus generics GenomicRanges ggplot2 ggrepel glue gridExtra gtable highr htmltools htmlwidgets httr igraph infotheo IRanges isoband iterators jquerylib jsonlite kernlab KernSmooth knitr labeling later lattice lazyeval lifecycle limma lme4 lmtest magrittr MASS Matrix MatrixGenerics MatrixModels matrixStats memoise mgcv microbenchmark mime minet minqa mixtools modelr nlme nloptr nnet numDeriv openssl otel pbkrtest permute pheatmap pillar pkgconfig plotly promises proxy purrr pwr qap quantreg R6 rappdirs rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen Rdpack RedeR reformulas registry rlang rmarkdown RTN RTNduals S4Arrays S4Vectors S7 sass scales scrutiny segmented Seqinfo seriation snow SparseArray SparseM statmod stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect timeDate tinytex TSP urca utf8 vctrs vegan viper viridisLite withr xfun XVector yaml zoo

RTNsurvival: multivariate survival analysis using transcriptional networks and regulons.

Rendered fromRTNsurvival.Rmdusingknitr::rmarkdown

Last update: 2025-07-23
Started: 2017-02-02

Help page	Topics
Performs survival analysis using transcriptional networks inferred by the RTN package.	RTNsurvival-package RTNsurvival
Semi-supervised hierarchical clustering	hclust_semisupervised
Preprocessing of TNS class objects	tni2tnsPreprocess tni2tnsPreprocess,TNI-method
TNS: An S4 class for survival analysis using transcriptional networks inferred by the RTN package.	TNS TNS-class
A pre-processed dataset for demonstration purposes only.	survival.data
Compute regulon activity by calling aREA (analytic Rank-based Enrichment Analysis) algorithm	tnsAREA3 tnsAREA3,TNS-method
Cox regression analysis for TNS class objects	tnsCox tnsCox,TNS-method
Cox regression analysis for dual regulons	tnsCoxInteraction tnsCoxInteraction,TNS-method
Get information from slots in a TNS object	tnsGet tnsGet,TNS-method
Compute regulon activity using 2-tailed Gene Set Enrichment Analysis	tnsGSEA2 tnsGSEA2,TNS-method
Survival analysis for dual regulons	tnsInteraction tnsInteraction,TNS-method
Kaplan-Meier analysis for TNS class objects	tnsKM tnsKM,TNS-method
Kaplan-Meier analysis for dual regulons	tnsKmInteraction tnsKmInteraction,TNS-method
Plot regulon activity and categorical covariates	tnsPlotCovariates tnsPlotCovariates,TNS-method
Cox plots for TNS class objects	tnsPlotCox tnsPlotCox,TNS-method
Plot results from Cox regression analysis for dual regulons	tnsPlotCoxInteraction tnsPlotCoxInteraction,TNS-method
Plot 2-tailed GSEA for a sample from a TNS	tnsPlotGSEA2 tnsPlotGSEA2,TNS-method
Kaplan-Meier plots for TNS class objects	tnsPlotKM tnsPlotKM,TNS-method
Plot results from Kaplan-Meier analysis for dual regulons	tnsPlotKmInteraction tnsPlotKmInteraction,TNS-method
Plot Subgroup Regulon Enrichment for TNS-class objects	tnsPlotSRE tnsPlotSRE,TNS-method
Subgroup Regulon Difference for TNS-class objects	tnsSRD tnsSRD,TNS-method
Subgroup Regulon Enrichment for TNS-class objects	tnsSRE tnsSRE,TNS-method
Sample stratification for a TNS object	tnsStratification

Package: RTNsurvival 1.37.0

RTNsurvival: Survival analysis using transcriptional networks inferred by the RTN package

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)