Man pages for gevaertlab/AMARETTO
Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis and Penalized Regression.

AMARETTO_CreateModuleDataAMARETTO_CreateModuleData
AMARETTO_CreateRegulatorProgramsAMARETTO_CreateRegulatorPrograms
AMARETTO_DownloadAMARETTO_Download
AMARETTO_EvaluateTestSetAMARETTO_EvaluateTestSet
AMARETTO_ExportResultsAMARETTO_ExportResults
AMARETTO_HTMLreportAMARETTO_HTMLreport
AMARETTO_InitializeAMARETTO_Initialize (version: reorder and filter MA_Matrix)
AMARETTO_LarsenBasedAMARETTO_LarsenBased
AMARETTO_LearnRegulatoryProgramsLarsenAMARETTO_LearnRegulatoryProgramsLarsen
AMARETTO_PreprocessAMARETTO_Preprocess
AMARETTO_ReassignGenesToClustersAMARETTO_ReassignGenesToClusters
AMARETTO_RunAMARETTO_Run
AMARETTO_VisualizeModuleAMARETTO_VisualizeModule
aprioraprior
BatchDataBatchData
Beta.NABeta.NA
bpriorbprior
build.designbuild.design
ComBat_NoFilesComBat_NoFiles
CreateRegulatorDataCreateRegulatorData
design.matdesign.mat
Driver_GenesDriver_Genes
filter.absentfilter.absent
FindTranscriptionallyPredictive_CNVFindTranscriptionallyPredictive_CNV
geneFilteringgeneFiltering
GeneSetDescriptionGeneSetDescription
get_firehoseDataget_firehoseData
GmtFromModulesGmtFromModules
HyperGTestGeneEnrichmentHyper Geometric Geneset Enrichement Test
int.epriorint.eprior
it.solit.sol
LL
list.batchlist.batch
MethylStatesMethylStates
postmeanpostmean
postvarpostvar
Preprocess_MAdataPreprocess_MAdata
printfprintf
ProcessedDataLIHCProcessedDataLIHC
randomColorrandomColor
readGMTreadGMT
Save_CancerSiteSave_CancerSite
TCGA_BatchCorrection_MolecularDataTCGA_BatchCorrection_MolecularData
TCGA_GENERIC_BatchCorrectionTCGA_GENERIC_BatchCorrection
TCGA_GENERIC_CheckBatchEffectTCGA_GENERIC_CheckBatchEffect
TCGA_GENERIC_CleanUpSampleNamesTCGA_GENERIC_CleanUpSampleNames
TCGA_GENERIC_GetSampleGroupsTCGA_GENERIC_GetSampleGroups
TCGA_GENERIC_MergeDataTCGA_GENERIC_MergeData
TCGA_Load_GISTICdataTCGA_Load_GISTICdata
TCGA_Load_MolecularDataTCGA_Load_MolecularData
trim.dattrim.dat
write_gctwrite_gct
gevaertlab/AMARETTO documentation built on Feb. 19, 2019, 4:15 a.m.