Man pages for broadinstitute/ImagingAMARETTO
ImagingAMARETTO: tools for interpreting multi-omics networks for relevance to clinical outcomes and radiographic and histopathology imaging-derived biomarkers
| all_module_KRUSKALWALLIS_test | Title |
| all_modules_cox_prop_hazard_test | Title |
| all_modules_PEARSONCOR_test | Title |
| all_modules_SPEARMANCOR_test | Title |
| all_module_TIMESERIESEDGE_test | Title all_module_TIMESERIESEDGE_test |
| all_module_WILCOXONRANKSUMPAIRED_test | Title |
| all_module_WILCOXONRANKSUM_test | Title |
| AMARETTO_CreateModuleData | AMARETTO_CreateModuleData |
| AMARETTO_CreateRegulatorPrograms | AMARETTO_CreateRegulatorPrograms |
| AMARETTO_Download | AMARETTO_Download |
| AMARETTO_EvaluateTestSet | AMARETTO_EvaluateTestSet |
| AMARETTO_ExportResults | AMARETTO_ExportResults |
| AMARETTO_HTMLCharacterisation | AMARETTO_HTMLCharacterisation |
| AMARETTO_HTMLreport | AMARETTO_HTMLreport |
| AMARETTOinit_all | AMARETTOinit_all |
| AMARETTO_Initialize | AMARETTO_Initialize (version: reorder and filter MA_Matrix) |
| AMARETTO_LarsenBased | AMARETTO_LarsenBased |
| AMARETTO_LearnRegulatoryProgramsLarsen | AMARETTO_LearnRegulatoryProgramsLarsen |
| AMARETTO_Preprocess | AMARETTO_Preprocess |
| AMARETTO_ReassignGenesToClusters | AMARETTO_ReassignGenesToClusters |
| AMARETTOresults_all | AMARETTOresults_all |
| AMARETTO_Run | AMARETTO_Run Function to run AMARETTO, a statistical... |
| AMARETTO_statistical_test | Title |
| AMARETTO_unite_results | Title |
| AMARETTO_VisualizeModule | AMARETTO_VisualizeModule |
| aprior | aprior |
| BatchData | BatchData |
| Beta.NA | Beta.NA |
| bprior | bprior |
| build.design | build.design |
| cacheResource | cacheResource |
| cAMARETTO_ColorOneModule | cAMARETTO_ColorOneModule Creates a network with one (or none)... |
| cAMARETTO_ExportResults | cAMARETTO_ExportResults |
| cAMARETTO_heatmap | cAMARETTO_heatmap Constructs a heatmap with the comparison... |
| cAMARETTO_HTML_Read | Title cAMARETTO_HTML_Read |
| cAMARETTO_HTMLreport | cAMARETTO_HTMLreport Creates a HTMLreport for the community... |
| cAMARETTO_IdentifyCom | cAMARETTO_IdentifyCom |
| cAMARETTO_InformationTable | cAMARETTO_InformationTable |
| cAMARETTO_ModuleNetwork | cAMARETTO_ModuleNetwork Creates a module network. |
| cAMARETTO_Read | cAMARETTO_Read Reads the AMARETTOinit and AMARETTOresults... |
| cAMARETTO_Results | cAMARETTO_Results To initiate the community AMARETTO this... |
| ComBat_NoFiles | ComBat_NoFiles |
| CommunityHyperLink | Title CommunityHyperLink |
| CommunityModuleTableCreate | Title CommunityModuleTableCreate |
| computeGisticURL | computeGisticURL |
| ComRunModGenInfo | Title ComRunModGenInfo |
| cox_prop_hazard_test | Title cox_prop_hazard_test |
| create_feature_matrix | Title create_feature_matrix |
| create_hgt_datatable | Title create_hgt_datatable |
| create_hgt_datatableC | Title create_hgt_datatableC |
| CreateHyperGeoTestAll | Title CreateHyperGeoTestAll |
| CreatePhenotypeTable | Title CreatePhenotypeTable |
| CreateRegulatorData | CreateRegulatorData |
| design.mat | design.mat |
| Driver_Genes | Driver_Genes |
| DriversSharedTbl | Title DriversSharedTbl |
| ExtractGenesInfo | Title ExtractGenesInfo |
| Extract_Genes_Modules_All | Title Extract_Genes_Modules_All |
| filter.absent | filter.absent |
| FindTranscriptionallyPredictive_CNV | FindTranscriptionallyPredictive_CNV |
| geneFiltering | geneFiltering |
| get_firehoseData | get_firehoseData |
| GmtFromModules | GmtFromModules |
| HGTGeneEnrichmentList | HGTGeneEnrichmentList Calculates the p-values for unranked... |
| HyperGeoEnrichmentTest | Title HyperGeoEnrichmentTest |
| HyperGTestGeneEnrichment | Hyper Geometric Geneset Enrichement Test |
| InitialCheckInputs | Title InitialCheckInputs |
| int.eprior | int.eprior |
| it.sol | it.sol |
| L | L |
| Lambda_Sequence | Lambda_Sequence |
| list.batch | list.batch |
| ModuleHyperLink | Title ModuleHyperLink |
| MsigdbMapping | MsigdbMapping |
| plot_run_history | Title plot_run_history |
| postmean | postmean |
| postvar | postvar |
| Preprocess_MAdata | Preprocess_MAdata |
| printf | printf |
| ProcessedDataCCLE | ProcessedDataCCLE |
| ProcessedDataLIHC | ProcessedDataLIHC |
| ProcessedDataTCGA | ProcessedDataTCGA |
| read_gct | read_gct |
| readGMT | readGMT |
| RunHyperLink | Title RunHyperLink |
| 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 |
