Package: RTNsurvival 1.31.0

Clarice Groeneveld

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

RTNsurvival is a tool for integrating regulons generated by the RTN package with survival information. For a given regulon, the 2-tailed GSEA approach computes a differential Enrichment Score (dES) for each individual sample, and the dES distribution of all samples is then used to assess the survival statistics for the cohort. There are two main survival analysis workflows: a Cox Proportional Hazards approach used to model regulons as predictors of survival time, and a Kaplan-Meier analysis assessing the stratification of a cohort based on the regulon activity. All plots can be fine-tuned to the user's specifications.

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

RTNsurvival_1.31.0.tar.gz
RTNsurvival_1.31.0.zip(r-4.5)RTNsurvival_1.31.0.zip(r-4.4)RTNsurvival_1.31.0.zip(r-4.3)
RTNsurvival_1.31.0.tgz(r-4.4-any)RTNsurvival_1.31.0.tgz(r-4.3-any)
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RTNsurvival.pdf |RTNsurvival.html✨
RTNsurvival/json (API)
NEWS

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

Peer review:

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

On BioConductor:RTNsurvival-1.31.0(bioc 3.21)RTNsurvival-1.30.0(bioc 3.20)

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

networkenrichmentsurvivalgeneregulationgenesetenrichmentnetworkinferencegraphandnetwork

3.30 score 9 scripts 197 downloads 1 mentions 20 exports 132 dependencies

Last updated 2 months agofrom:d6d7932837. Checks:OK: 3 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 30 2024
R-4.5-winNOTENov 30 2024
R-4.5-linuxNOTENov 30 2024
R-4.4-winNOTENov 30 2024
R-4.4-macNOTENov 30 2024
R-4.3-winOKNov 30 2024
R-4.3-macOKNov 30 2024

Exports:hclust_semisupervisedtni2tnsPreprocesstnsAREA3tnsCoxtnsCoxInteractiontnsGettnsGSEA2tnsInteractiontnsKMtnsKmInteractiontnsPlotCovariatestnsPlotCoxtnsPlotCoxInteractiontnsPlotGSEA2tnsPlotKMtnsPlotKmInteractiontnsPlotSREtnsSRDtnsSREtnsStratification

Dependencies:abindaskpassbackportsbase64encBiobaseBiocGenericsbootbroombslibcachemcarcarDataclassclicolorspacecowplotcpp11crayoncrosstalkcurldata.tableDelayedArrayDerivdigestdoBydplyrdunn.teste1071eggevaluatefansifarverfastmapfontawesomeFormulafsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegridExtragtablehighrhtmltoolshtmlwidgetshttrigraphinfotheoIRangesisobandjquerylibjsonlitekernlabKernSmoothknitrlabelinglaterlatticelazyevallifecyclelimmalme4magrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmicrobenchmarkmimeminetminqamixtoolsmodelrmunsellnlmenloptrnnetnumDerivopensslpbkrtestpheatmappillarpkgconfigplotlypromisesproxypurrrpwrquantregR6rappdirsRColorBrewerRcppRcppEigenRedeRrlangrmarkdownRTNRTNdualsS4ArraysS4VectorssassscalessegmentedsnowSparseArraySparseMstatmodstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttinytexUCSC.utilsutf8vctrsviperviridisLitewithrxfunXVectoryamlzlibbioc

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 Nov 30 2024.

Last update: 2020-11-10
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