Files in broadinstitute/ImagingAMARETTO

ImagingAMARETTO: tools for interpreting multi-omics networks for relevance to clinical outcomes and radiographic and histopathology imaging-derived biomarkers

R/amaretto_download.R R/amaretto_functions.R R/amaretto_htmlphenotypes.R R/amaretto_htmlreport.R R/amaretto_initialize.R R/amaretto_phenotype_analysis.R R/amaretto_preprocess.R R/amaretto_run.R R/amaretto_vizualize.R R/cAMARETTO_ColorOneModule.R R/cAMARETTO_DataReadDownload.R R/cAMARETTO_HTMLreport.R R/cAMARETTO_InformationTable.R R/cAMARETTO_Results.R R/cAMARETTO_heatmap.R R/cAMARETTO_identifycom.R R/cAMARETTO_modulenetwork.R R/data.R README.md inst/templates/TemplateIndexPage.Rmd inst/templates/TemplateIndexPage_AllGenes.Rmd inst/templates/TemplateIndexPage_GenesetsEnrichment.Rmd inst/templates/TemplateIndexPage_GenesetsEnrichment_cp.Rmd inst/templates/TemplateIndexPage_GenesetsEnrichment_gp.Rmd inst/templates/TemplateIndexPage_Overview.Rmd inst/templates/TemplateIndexPage_PhenoAssociation.Rmd inst/templates/TemplateIndexPage_PhenoAssociationImg.Rmd inst/templates/TemplatePhenotypesIndex.Rmd inst/templates/TemplatePhenotypesModule.Rmd inst/templates/TemplateSurvivalIndex.Rmd inst/templates/TemplateSurvivalModule.Rmd inst/templates/module_templates/TemplateReportModule.Rmd inst/templatesC/TemplateIndexPage.Rmd inst/templatesC/TemplateIndexPage_AllCommunities.Rmd inst/templatesC/TemplateIndexPage_AllGenes.Rmd inst/templatesC/TemplateIndexPage_Drivers.Rmd inst/templatesC/TemplateIndexPage_Drivers2.Rmd inst/templatesC/TemplateIndexPage_GenesetsEnrichment.Rmd inst/templatesC/TemplateIndexPage_GenesetsEnrichment_cp.Rmd inst/templatesC/TemplateIndexPage_GenesetsEnrichment_gp.Rmd inst/templatesC/TemplateIndexPage_PhenoAssociation.Rmd inst/templatesC/TemplateIndexPage_PhenoAssociationImg.Rmd inst/templatesC/TemplateIndexPage_RunsInfo.Rmd inst/templatesC/community_page_template/TemplateCommunityPage.Rmd man/AMARETTO_CreateModuleData.Rd man/AMARETTO_CreateRegulatorPrograms.Rd man/AMARETTO_Download.Rd man/AMARETTO_EvaluateTestSet.Rd man/AMARETTO_ExportResults.Rd man/AMARETTO_HTMLCharacterisation.Rd man/AMARETTO_HTMLreport.Rd man/AMARETTO_Initialize.Rd man/AMARETTO_LarsenBased.Rd man/AMARETTO_LearnRegulatoryProgramsLarsen.Rd man/AMARETTO_Preprocess.Rd man/AMARETTO_ReassignGenesToClusters.Rd man/AMARETTO_Run.Rd man/AMARETTO_VisualizeModule.Rd man/AMARETTO_statistical_test.Rd man/AMARETTO_unite_results.Rd man/AMARETTOinit_all.Rd man/AMARETTOresults_all.Rd man/BatchData.Rd man/Beta.NA.Rd man/ComBat_NoFiles.Rd man/ComRunModGenInfo.Rd man/CommunityHyperLink.Rd man/CommunityModuleTableCreate.Rd man/CreateHyperGeoTestAll.Rd man/CreatePhenotypeTable.Rd man/CreateRegulatorData.Rd man/Driver_Genes.Rd man/DriversSharedTbl.Rd man/ExtractGenesInfo.Rd man/Extract_Genes_Modules_All.Rd man/FindTranscriptionallyPredictive_CNV.Rd man/GmtFromModules.Rd man/HGTGeneEnrichmentList.Rd man/HyperGTestGeneEnrichment.Rd man/HyperGeoEnrichmentTest.Rd man/InitialCheckInputs.Rd man/L.Rd man/Lambda_Sequence.Rd man/ModuleHyperLink.Rd man/MsigdbMapping.Rd man/Preprocess_MAdata.Rd man/ProcessedDataCCLE.Rd man/ProcessedDataLIHC.Rd man/ProcessedDataTCGA.Rd man/RunHyperLink.Rd man/Save_CancerSite.Rd man/TCGA_BatchCorrection_MolecularData.Rd man/TCGA_GENERIC_BatchCorrection.Rd man/TCGA_GENERIC_CheckBatchEffect.Rd man/TCGA_GENERIC_CleanUpSampleNames.Rd man/TCGA_GENERIC_GetSampleGroups.Rd man/TCGA_GENERIC_MergeData.Rd man/TCGA_Load_GISTICdata.Rd man/TCGA_Load_MolecularData.Rd man/all_module_KRUSKALWALLIS_test.Rd man/all_module_TIMESERIESEDGE_test.Rd man/all_module_WILCOXONRANKSUMPAIRED_test.Rd man/all_module_WILCOXONRANKSUM_test.Rd man/all_modules_PEARSONCOR_test.Rd man/all_modules_SPEARMANCOR_test.Rd man/all_modules_cox_prop_hazard_test.Rd man/aprior.Rd man/bprior.Rd man/build.design.Rd man/cAMARETTO_ColorOneModule.Rd man/cAMARETTO_ExportResults.Rd man/cAMARETTO_HTML_Read.Rd man/cAMARETTO_HTMLreport.Rd man/cAMARETTO_IdentifyCom.Rd man/cAMARETTO_InformationTable.Rd man/cAMARETTO_ModuleNetwork.Rd man/cAMARETTO_Read.Rd man/cAMARETTO_Results.Rd man/cAMARETTO_heatmap.Rd man/cacheResource.Rd man/computeGisticURL.Rd man/cox_prop_hazard_test.Rd man/create_feature_matrix.Rd man/create_hgt_datatable.Rd man/create_hgt_datatableC.Rd man/design.mat.Rd man/filter.absent.Rd man/geneFiltering.Rd man/get_firehoseData.Rd man/int.eprior.Rd man/it.sol.Rd man/list.batch.Rd man/plot_run_history.Rd man/postmean.Rd man/postvar.Rd man/printf.Rd man/readGMT.Rd man/read_gct.Rd man/trim.dat.Rd man/write_gct.Rd