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
AMARETTO_LarsenBased	AMARETTO_LarsenBased
AMARETTO_LearnRegulatoryProgramsLarsen	AMARETTO_LearnRegulatoryProgramsLarsen
AMARETTO_Preprocess	AMARETTO_Preprocess
AMARETTO_ReassignGenesToClusters	AMARETTO_ReassignGenesToClusters
AMARETTO_Run	AMARETTO_Run
AMARETTO_VisualizeModule	AMARETTO_VisualizeModule
aprior	aprior
BatchData	BatchData
Beta.NA	Beta.NA
bprior	bprior
build.design	build.design
cacheResource	cacheResource
ComBat_NoFiles	ComBat_NoFiles
computeGisticURL	computeGisticURL
CreateRegulatorData	CreateRegulatorData
design.mat	design.mat
Driver_Genes	Driver_Genes
filter.absent	filter.absent
FindTranscriptionallyPredictive_CNV	FindTranscriptionallyPredictive_CNV
geneFiltering	geneFiltering
GeneSetDescription	GeneSetDescription
get_firehoseData	get_firehoseData
GmtFromModules	GmtFromModules
HyperGTestGeneEnrichment	HyperGTestGeneEnrichment
int.eprior	int.eprior
it.sol	it.sol
L	L
Lambda_Sequence	Lambda_Sequence
list.batch	list.batch
MsigdbMapping	MsigdbMapping
plot_run_history	plot_run_history
postmean	postmean
postvar	postvar
Preprocess_MAdata	Preprocess_MAdata
printf	printf
ProcessedDataLIHC	ProcessedDataLIHC
readGMT	readGMT
read_gct	read_gct
Save_CancerSite	Save_CancerSite
TCGA_BatchCorrection_MolecularData	TCGA_BatchCorrection_MolecularData
TCGA_GENERIC_BatchCorrection	TCGA_GENERIC_BatchCorrection
TCGA_GENERIC_CheckBatchEffect	TCGA_GENERIC_CheckBatchEffect
TCGA_GENERIC_CleanUpSampleNames	TCGA_GENERIC_CleanUpSampleNames
TCGA_GENERIC_GetSampleGroups	TCGA_GENERIC_GetSampleGroups
TCGA_GENERIC_MergeData	TCGA_GENERIC_MergeData
TCGA_Load_GISTICdata	TCGA_Load_GISTICdata
TCGA_Load_MolecularData	TCGA_Load_MolecularData
trim.dat	trim.dat
write_gct	write_gct
