# Empirical Bayesian approach to mutational signature discovery

## Documentation for package ‘signeR’ version 2.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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
genCountMatrixFromVcf | count matrix and opportinity matrix generators
genOpportunityFromGenome | count matrix and opportinity 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