Differential Epigenetic Coregulation Test

boxM | Box's M-test |

boxM_fast | Box's M-test |

boxM_permute | Box's M-test |

collapseClusters | Collapse clusters based on jaccard index |

combineResults | Combine results into a single data.frame |

corrMatrix.test | Test difference between two correlation matricies |

corSubsetPairs | Compute correlations between pairs of features |

countClusters-methods | Count clusters on each chromosome |

createClusters | Create cluster from list of hclust objects |

createCorrelationMatrix | Create correlation matrix |

decorateData | Simulated data to show correlation clustering |

delaneau.score | Score impact of each sample on correlation sturucture |

delaneau.test | Test association between correlation sturucture and variable |

dot-evalDiffCorr | Internal .evalDiffCorr |

epiclust-class | Class epiclust |

epiclustDiscreteList-class | Class epiclustDiscreteList |

epiclustDiscreteListContain-class | Class epiclustDiscreteListContain |

epiclustList-class | Class epiclustList |

evalDiffCorr-methods | Evaluate Differential Correlation |

evaluateCorrDecay | Evaluate the decay of correlation versus distance between... |

extractCorrelationScores | Extract sample-level correlation scores |

filterClusters | Extract subset of clusters |

getClusterNames | Get name of each cluster |

getClusterRanges | Get genome coordinates for each cluster |

get_exon_coords | Get coordinates of exons |

getFeaturesInCluster | Get feature names in selected cluster |

getFeaturesInClusterList | Get feature names in selected cluster |

getPeakDistances | Compute distance between peaks |

getSubset-methods | Extract subset of data points |

ggplot_by_sampling | Plot by subsampling in each bin |

jaccard | Evaluate Jaccard index |

makeImageRect | Convert correlation matrix into triangle plot |

plotClusterSegments | Plot cluster segments |

plotCompareCorr | Plot two correlation matrices together |

plotCorrDecay | Plot correlation delay |

plotCorrTriangle | Plot triangle of correlation matrix |

plotDecorate | Plot decorate analysis |

plotDensityPoints | Plot density as color, add outlier points |

plotEnsGenes | Plot ENSEMBL genes |

plotGenes | Plot genes from a specified region of the human genome. |

plotPairwiseScatter | Scatter plot of all pairs of variables stratified by test... |

plotScatterPairs | Scatter plot of all pairs of variables stratified by test... |

retainClusters | Retain clusters by applying filter |

runFastStat | Test difference in correlation using closed form tests |

runOrderedClustering | Run hierarchical clustering preserving order |

runOrderedClusteringGenome | Run hierarchical clustering preserving order |

runPermutedData | Run hierarchical clustering permuting features |

scoreClusters | Compute scores for each cluster |

sLEDresults-class | An S4 class that stores results of sLED analysis |

sle.score | Score impact of each sample on sparse leading eigen-value |

sle.test | Test association between sparse leading eigen-value and... |

sub-epiclustDiscreteListContain-ANY-ANY-ANY-method | Allow subsetting of epiclustDiscreteListContain |

summary-sLEDresults-method | Summarize sLED analysis |

whichCluster | Find which cluster a peak is in |

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