| signeR-package | Empirical Bayesian approach to mutational signature discovery |
| Average_exp | SignExp class methods |
| Average_exp-method | SignExp class methods |
| Average_sign | SignExp class methods |
| Average_sign-method | SignExp class methods |
| BICboxplot | signeR plot functions |
| cosmic_data | COSMIC Mutational Signatures |
| DiffExp | Differential Exposure Analysis |
| DiffExp-method | Differential Exposure Analysis |
| ExposureBarplot | signeR plot functions |
| ExposureBarplot-method | signeR plot functions |
| ExposureBoxplot | signeR plot functions |
| ExposureBoxplot-method | signeR plot functions |
| ExposureClassify | Classify samples by exposure levels |
| ExposureClassify-method | Classify samples by exposure levels |
| ExposureClassifyCV | k-fold cross-validation of sample classifcation by exposure levels |
| ExposureClassifyCV-method | k-fold cross-validation of sample classifcation by exposure levels |
| ExposureCorrelation | Exposure correlation analysis (given a known sample feature) |
| ExposureCorrelation-method | Exposure correlation analysis (given a known sample feature) |
| ExposureGLM | Exposure Generalized Linear Model |
| ExposureGLM-method | Exposure Generalized Linear Model |
| ExposureHeat | signeR plot functions |
| ExposureHeat-method | signeR plot functions |
| ExposureSurvival | Exposure survival analysis |
| ExposureSurvival-method | Exposure survival analysis |
| ExposureSurvModel | Exposure Cox model |
| ExposureSurvModel-method | Exposure Cox model |
| FuzzyClustExp | Fuzzy Clustering of exposure data |
| FuzzyClustExp-method | Fuzzy Clustering of exposure data |
| genCountMatrixFromMAF | count matrix and opportunity matrix generators |
| genCountMatrixFromVcf | count matrix and opportunity matrix generators |
| genOpportunityFromGenome | count matrix and opportunity matrix generators |
| HClustExp | Hierarchical Clustering of exposure data |
| HClustExp-method | Hierarchical Clustering of exposure data |
| Median_exp | SignExp class methods |
| Median_exp-method | SignExp class methods |
| Median_sign | SignExp class methods |
| Median_sign-method | SignExp class methods |
| Normalize | SignExp class methods |
| Normalize-method | SignExp class methods |
| Paths | signeR plot functions |
| Paths-method | signeR plot functions |
| Reorder_mutations | SignExp class methods |
| Reorder_mutations-method | SignExp class methods |
| Reorder_samples | SignExp class methods |
| Reorder_samples-method | SignExp class methods |
| Reorder_signatures | SignExp class methods |
| Reorder_signatures-method | SignExp class methods |
| setMutations | SignExp class methods |
| setMutations-method | SignExp class methods |
| setSamples | SignExp class methods |
| setSamples-method | SignExp class methods |
| signeR | signeR |
| signeRFlow | Launch signeRFlow R Shiny web app |
| SignExp | SignExp class |
| SignExp-class | SignExp class |
| SignHeat | signeR plot functions |
| SignHeat-method | signeR plot functions |
| SignPlot | signeR plot functions |
| SignPlot-method | signeR plot functions |
| tcga_similarities | TCGA Cosmic similarities |
| tcga_tumors | TCGA tumors used on TCGA Explorer |