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

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Documentation for package ‘AMARETTO’ version 1.16.0

• 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