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| Chicago-package | CHiCAGO: Capture Hi-C Analysis of Genomic Organization |
| cdUnitTest | ChicagoData object for unit testing |
| Chicago | CHiCAGO: Capture Hi-C Analysis of Genomic Organization |
| chicagoData | The 'chicagoData' class. |
| chicagoPipeline | CHiCAGO pipeline function |
| copyCD | Copy chicagoData object |
| defaultSettings | Default CHiCAGO settings |
| estimateBrownianComponent | Estimate Brownian background component. |
| estimateBrownianNoise | Estimate Brownian background component. |
| estimateDistFun | Estimate the Distance Function |
| estimateTechnicalNoise | Estimate Technical Noise |
| exportResults | Export Results |
| exportToGI | Export Results |
| getPvals | Get P-values |
| getScores | Get CHiCAGO scores. |
| getSkOnly | Get S_k factors from multiple replicates |
| intData | The 'chicagoData' class. |
| intData-method | The 'chicagoData' class. |
| intData<- | The 'chicagoData' class. |
| intData<--method | The 'chicagoData' class. |
| mergeSamples | Merge samples together. |
| modifySettings | Modify Settings |
| normaliseBaits | Normalise Baits |
| normaliseOtherEnds | Normalise Other Ends |
| overlapFragWithFeatures | Overlap Other-Ends with Features |
| params | The 'chicagoData' class. |
| params-method | The 'chicagoData' class. |
| params<- | The 'chicagoData' class. |
| params<--method | The 'chicagoData' class. |
| peakEnrichment4Features | Enrichment for Features |
| plotBaits | Plot Baits |
| plotDistFun | Plot the Distance Function |
| readAndMerge | Read And Merge |
| readSample | Read Sample |
| setExperiment | Set Experiment |
| settings | The 'chicagoData' class. |
| settings-method | The 'chicagoData' class. |