API for MOCHA
Modeling for Single-Cell Open Chromatin Analysis
| Global functions | |
|---|---|
| .callOpenTiles | Source code |
| .callOpenTiles_ArchR | Man page Source code |
| .callOpenTiles_default | Source code |
| .counts_plot_default_theme | Man page |
| .gene_plot_theme | Man page |
| .getSpacing | Source code |
| .getTrackLabels | Source code |
| .plot_GRanges | Source code |
| .setUpLegend | Source code |
| EnrichedRanges | Source code |
| GRangesToString | Man page |
| MotifEnrichment | Man page Source code |
| MotifSetEnrichmentAnalysis | Man page Source code |
| PHyperLigandTF | Source code |
| Spearman | Source code |
| StringsToGRanges | Man page Source code |
| TwoPart | Source code |
| ZISpearman | Source code |
| addAccessibilityShift | Man page Source code |
| addMotifSet | Man page Source code |
| annotateTiles | Man page Source code |
| averageCoverage | Source code |
| breaks_to_scaledbreaks | Source code |
| bulkDimReduction | Man page Source code |
| bulkUMAP | Man page Source code |
| calculateCoverage | Source code |
| calculateMeanDiff | Source code |
| calculate_intensities | Source code |
| callOpenTiles | Man page |
| callOpenTiles,ArchRProject-method | Man page |
| callOpenTiles,GRangesList-method | Man page |
| callOpenTiles,list-method | Man page |
| callTilesBySample | Source code |
| cellTypeDF | Source code |
| cleanup_breaks | Source code |
| co_accessibility | Source code |
| combineRagged | Source code |
| combineSampleTileMatrix | Man page Source code |
| countdf_to_region | Source code |
| counts_plot_samples | Source code |
| determine_dynamic_range | Source code |
| differentialsToGRanges | Man page |
| dynamic_bins | Source code |
| estimate_differential_accessibility | Source code |
| exampleBlackList | Man page |
| exampleCellColData | Man page |
| exampleFragments | Man page |
| exportCoverage | Man page Source code |
| exportDifferentials | Man page Source code |
| exportMotifs | Man page Source code |
| exportOpenTiles | Man page Source code |
| exportSmoothedInsertions | Man page Source code |
| extractErrorFromConsensusTiles | Man page Source code |
| extractRegion | Man page Source code |
| extractVariable | Source code |
| filterCoAccessibleLinks | Man page Source code |
| finalModelObject | Man page |
| getAltTSS | Man page Source code |
| getAnnotationDbFromInstalledPkgname | Man page |
| getCellPopMatrix | Man page Source code |
| getCellTypeTiles | Man page |
| getCellTypes | Man page |
| getCoAccessibleLinks | Man page Source code |
| getCoverage | Man page Source code |
| getDifferentialAccessibleTiles | Man page Source code |
| getIntensityThreshold | Man page Source code |
| getModelValues | Man page Source code |
| getPopFrags | Man page Source code |
| getPromoterGenes | Man page |
| getSampleCellTypeMetadata | Man page |
| getSampleTileMatrix | Man page Source code |
| getSequencingBias | Man page Source code |
| getSpecificCoverage | Source code |
| get_gene_plot | Source code |
| get_motifs_in_region | Source code |
| get_promoter_range | Source code |
| individualZIGLMM | Source code |
| make_prediction | Source code |
| mergeTileResults | Man page Source code |
| packMOCHA | Man page Source code |
| pilotLMEM | Man page Source code |
| pilotZIGLMM | Man page Source code |
| plotConsensus | Man page Source code |
| plotIntensityDistribution | Man page Source code |
| plotRegion | Man page Source code |
| processModelOutputs | Source code |
| renameCellTypes | Man page Source code |
| runCoAccessibility | Source code |
| runLMEM | Man page Source code |
| runZIGLMM | Man page Source code |
| sampleDataFromCellColData | Source code |
| simplifiedConsensusTiles | Man page Source code |
| simplifiedFragments | Source code |
| simplifiedSampleTile | Source code |
| simplifiedTilesBySample | Source code |
| singlePopulationConsensusTiles | Man page Source code |
| singlePopulationSampleTileMatrix | Man page Source code |
| splitFragsByCellPop | Source code |
| subsetMOCHAObject | Man page Source code |
| subset_Frag | Source code |
| testCoAccessibility | Man page Source code |
| testCoAccessibilityChromVar | Man page Source code |
| testCoAccessibilityRandom | Man page Source code |
| unpackMOCHA | Man page Source code |
| validRegionString | Source code |
| varZIGLMM | Man page Source code |
| weightedZISpearman | Source code |
| youden_threshold | Man page |
