Empirical Bayesian approach to mutational signature discovery


[Up] [Top]

Documentation for package ‘signeR’ version 2.0.2

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