Empirical Bayesian approach to mutational signature discovery

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Documentation for package ‘signeR’ version 2.11.1

• 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
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