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| dbLoadingAttempt | Object to store SCENIC settings |
| dbVersion | Object to store SCENIC settings |
| defaultDbNames | Default databases by organism |
| export2scope | export2scope |
| exportsForArboreto | exportsForArboreto (alias: exportsForGRNBoost) |
| geneFiltering | geneFiltering |
| getDatabases | Object to store SCENIC settings |
| getDatabases-method | Object to store SCENIC settings |
| getDatasetInfo | Object to store SCENIC settings |
| getDatasetInfo-method | Object to store SCENIC settings |
| getDbAnnotations | getDbAnnotations |
| getDbTfs | getDbTfs |
| getIntName | Object to store SCENIC settings |
| getIntName-method | Object to store SCENIC settings |
| getOutName | Object to store SCENIC settings |
| getOutName-method | Object to store SCENIC settings |
| getRegulonName | getRegulonName |
| getSettings | Object to store SCENIC settings |
| getSettings-method | Object to store SCENIC settings |
| getTF | getTF |
| importArboreto | importArboreto |
| importAUCfromText | importAUCfromText |
| initializeScenic | Object to store SCENIC settings |
| loadFile | Object to store SCENIC settings |
| loadFile-method | Object to store SCENIC settings |
| loadInt | Object to store SCENIC settings |
| loadInt-method | Object to store SCENIC settings |
| onlyNonDuplicatedExtended | onlyNonDuplicatedExtended |
| plotTsne_AUCellApp | plotTsne_AUCellApp |
| plotTsne_AUCellHtml | plotTsne_AUCellHtml |
| plotTsne_compareSettings | plotTsne_compareSettings |
| plotTsne_rgb | plotTsne_rgb |
| regulonsToGeneLists | regulonsToGeneSet |
| regulon_plotExpression | regulon_plotExpression |
| runCorrelation | runCorrelation |
| runGenie3 | runGenie3 |
| runSCENIC_1_coexNetwork2modules | runSCENIC_1_coexNetwork2modules |
| runSCENIC_2_createRegulons | runSCENIC_2_createRegulons |
| runSCENIC_3_scoreCells | runSCENIC_3_scoreCells |
| runSCENIC_4_aucell_binarize | runSCENIC_4_aucell_binarize |
| ScenicOptions | Object to store SCENIC settings |
| ScenicOptions-class | Object to store SCENIC settings |
| selectRegulons | selectRegulons |
| show | Object to store SCENIC settings |
| show-method | Object to store SCENIC settings |
| tsneAUC | tsneAUC |
| viewMotifs | viewMotifs |