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