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✨
card.svg |card.png
RTNsurvival/json (API)
NEWS

# 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.

networkenrichmentsurvivalgeneregulationgenesetenrichmentnetworkinferencegraphandnetwork

3.78 score 15 scripts 384 downloads 1 mentions 20 exports 153 dependencies

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

TargetResultTimeFilesSyslog
bioc-checksERROR153
linux-devel-x86_64NOTE353
source / vignettesOK290
linux-release-x86_64NOTE330
macos-release-arm64NOTE215
macos-oldrel-arm64NOTE240
windows-develNOTE254
windows-releaseNOTE242
windows-oldrelNOTE249
wasm-releaseOK169

Exports:hclust_semisupervisedtni2tnsPreprocesstnsAREA3tnsCoxtnsCoxInteractiontnsGettnsGSEA2tnsInteractiontnsKMtnsKmInteractiontnsPlotCovariatestnsPlotCoxtnsPlotCoxInteractiontnsPlotGSEA2tnsPlotKMtnsPlotKmInteractiontnsPlotSREtnsSRDtnsSREtnsStratification

Dependencies:abindaskpassbackportsbase64encBiobaseBiocGenericsbootbroombslibcacachemcarcarDataclasscliclustercodetoolscolorspacecorrrcowplotcpp11crosstalkcurldata.tableDelayedArrayDerivdigestdoBydplyrdunn.teste1071eggevaluatefarverfastmapfontawesomeforeachforecastFormulafracdifffsgclusgenericsGenomicRangesggplot2ggrepelgluegridExtragtablehighrhtmltoolshtmlwidgetshttrigraphinfotheoIRangesisobanditeratorsjquerylibjsonlitekernlabKernSmoothknitrlabelinglaterlatticelazyevallifecyclelimmalme4lmtestmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmicrobenchmarkmimeminetminqamixtoolsmodelrnlmenloptrnnetnumDerivopensslotelpbkrtestpermutepheatmappillarpkgconfigplotlypromisesproxypurrrpwrqapquantregR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackRedeRreformulasregistryrlangrmarkdownRTNRTNdualsS4ArraysS4VectorsS7sassscalesscrutinysegmentedSeqinfoseriationsnowSparseArraySparseMstatmodstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttimeDatetinytexTSPurcautf8vctrsveganviperviridisLitewithrxfunXVectoryamlzoo

RTNsurvival: multivariate survival analysis using transcriptional networks and regulons.

Clarice S Groeneveld, Vinícius S Chagas, Gordon Robertson, Kerstin B Meyer, Mauro AA Castro.

Rendered fromRTNsurvival.Rmdusingknitr::rmarkdownon May 30 2026.

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

Readme and manuals

Help Manual

Help pageTopics
Performs survival analysis using transcriptional networks inferred by the RTN package.RTNsurvival-package RTNsurvival
Semi-supervised hierarchical clusteringhclust_semisupervised
Preprocessing of TNS class objectstni2tnsPreprocess 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) algorithmtnsAREA3 tnsAREA3,TNS-method
Cox regression analysis for TNS class objectstnsCox tnsCox,TNS-method
Cox regression analysis for dual regulonstnsCoxInteraction tnsCoxInteraction,TNS-method
Get information from slots in a TNS objecttnsGet tnsGet,TNS-method
Compute regulon activity using 2-tailed Gene Set Enrichment AnalysistnsGSEA2 tnsGSEA2,TNS-method
Survival analysis for dual regulonstnsInteraction tnsInteraction,TNS-method
Kaplan-Meier analysis for TNS class objectstnsKM tnsKM,TNS-method
Kaplan-Meier analysis for dual regulonstnsKmInteraction tnsKmInteraction,TNS-method
Plot regulon activity and categorical covariatestnsPlotCovariates tnsPlotCovariates,TNS-method
Cox plots for TNS class objectstnsPlotCox tnsPlotCox,TNS-method
Plot results from Cox regression analysis for dual regulonstnsPlotCoxInteraction tnsPlotCoxInteraction,TNS-method
Plot 2-tailed GSEA for a sample from a TNStnsPlotGSEA2 tnsPlotGSEA2,TNS-method
Kaplan-Meier plots for TNS class objectstnsPlotKM tnsPlotKM,TNS-method
Plot results from Kaplan-Meier analysis for dual regulonstnsPlotKmInteraction tnsPlotKmInteraction,TNS-method
Plot Subgroup Regulon Enrichment for TNS-class objectstnsPlotSRE tnsPlotSRE,TNS-method
Subgroup Regulon Difference for TNS-class objectstnsSRD tnsSRD,TNS-method
Subgroup Regulon Enrichment for TNS-class objectstnsSRE tnsSRE,TNS-method
Sample stratification for a TNS objecttnsStratification