Files in AMARETTO

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

README.md R/amaretto_preprocess.R R/amaretto_htmlreport.R R/amaretto_run.R R/amaretto_vizualize.R R/amaretto_download.R R/amaretto_initialize.R R/data.R R/amaretto_functions.R vignettes/amaretto.Rmd man/TCGA_GENERIC_MergeData.Rd man/int.eprior.Rd man/AMARETTO_HTMLreport.Rd man/ComBat_NoFiles.Rd man/AMARETTO_LarsenBased.Rd man/TCGA_GENERIC_BatchCorrection.Rd man/Beta.NA.Rd man/TCGA_GENERIC_GetSampleGroups.Rd man/AMARETTO_CreateModuleData.Rd man/AMARETTO_ReassignGenesToClusters.Rd man/TCGA_GENERIC_CheckBatchEffect.Rd man/filter.absent.Rd man/GeneSetDescription.Rd man/MsigdbMapping.Rd man/L.Rd man/ProcessedDataLIHC.Rd man/GmtFromModules.Rd man/it.sol.Rd man/HyperGTestGeneEnrichment.Rd man/AMARETTO_VisualizeModule.Rd man/postvar.Rd man/write_gct.Rd man/AMARETTO_CreateRegulatorPrograms.Rd man/TCGA_Load_GISTICdata.Rd man/computeGisticURL.Rd man/aprior.Rd man/TCGA_Load_MolecularData.Rd man/TCGA_GENERIC_CleanUpSampleNames.Rd man/plot_run_history.Rd man/Preprocess_MAdata.Rd man/AMARETTO_ExportResults.Rd man/get_firehoseData.Rd man/readGMT.Rd man/AMARETTO_Initialize.Rd man/BatchData.Rd man/AMARETTO_Download.Rd man/build.design.Rd man/printf.Rd man/Save_CancerSite.Rd man/design.mat.Rd man/bprior.Rd man/read_gct.Rd man/AMARETTO_Run.Rd man/AMARETTO_EvaluateTestSet.Rd man/Lambda_Sequence.Rd man/FindTranscriptionallyPredictive_CNV.Rd man/CreateRegulatorData.Rd man/Driver_Genes.Rd man/postmean.Rd man/TCGA_BatchCorrection_MolecularData.Rd man/AMARETTO_Preprocess.Rd man/AMARETTO_LearnRegulatoryProgramsLarsen.Rd man/trim.dat.Rd man/list.batch.Rd man/cacheResource.Rd man/geneFiltering.Rd tests/testthat.R tests/testthat/test_AMARETTO.R inst/doc/amaretto.R inst/doc/amaretto.Rmd inst/templates/TemplateReportModule.Rmd inst/templates/TemplateIndexPage.Rmd