# Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis and Penalized Regression

## Documentation for package ‘AMARETTO’ version 1.4.0

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

## Help Pages

AMARETTO_CreateModuleData | AMARETTO_CreateModuleData
AMARETTO_CreateRegulatorPrograms | AMARETTO_CreateRegulatorPrograms
AMARETTO_Download | AMARETTO_Download
AMARETTO_EvaluateTestSet | AMARETTO_EvaluateTestSet
AMARETTO_ExportResults | AMARETTO_ExportResults
AMARETTO_HTMLreport | AMARETTO_HTMLreport
AMARETTO_Initialize | AMARETTO_Initialize (version: reorder and filter MA_Matrix)
AMARETTO_Preprocess | AMARETTO_Preprocess
AMARETTO_Run | AMARETTO_Run Function to run AMARETTO, a statistical algorithm to identify cancer drivers by integrating a variety of omics data from cancer and normal tissue.
AMARETTO_VisualizeModule | AMARETTO_VisualizeModule
BatchData | BatchData
Driver_Genes | Driver_Genes
MsigdbMapping | MsigdbMapping
plot_run_history | Title plot_run_history
ProcessedDataLIHC | ProcessedDataLIHC
read_gct | read_gct