Identification of co-regulated genomic regions based on correlation analysis

AccMatrix-class | AccMatrix class that is used to store accessibility matrices |

compareCorCoeffs | This function returns p-values assessing the difference... |

compareCorDistributions | This function returns p-values assessing the difference... |

CorMatrix-class | CorMatrix class that is used to store correlation matrices |

countReads | This function counts reads in a GRanges object that fall into... |

cropAccMatrix | This function crops accessibility matrices |

cropCorMatrix | This function crops correlation matrices |

getAccLUT | This function makes a color LUT for accessibility matrices |

getCIs | This function returns confidence intervals |

getCorBackground | This function returns the background correlation obtained... |

getCorLUT | This function makes a color LUT for correlation matrices |

getCorRanges | This function returns bootstrapped correlation coefficients |

getPEPairs | This function returns promoter-enhancer (P-E) pairs based on... |

makeAccMatrix | This function makes accessibility matrices from a set of BED... |

makeCorMatrix | This function makes a correlation matrix from two... |

makeGenomeTiles | This function makes tiles for the complete hg19 genome |

makeIPCHist | This function makes a histogram for the number of... |

makeIPCStats | Calculate statistics for the number of integrations per cell |

makeIPRHist | This function makes a histogram for the number of cells with... |

makeIPRStats | Calculate statistics for the number of integrations per ROI |

makeTiles | This function makes tiles for a particular chromosome of the... |

PEPairs-class | PEPairs class that is used to store sets of promoter-enhancer... |

readBed | This function reads a BED file and stores the reads in a... |

removeEmptyRows | This function removes empty rows from accessibility matrices |

removeRowsBelowCutoff | This function removes rows below a certain cutoff from... |

saveImage | This function saves a matrix as an image |

scaleAccMatrix | This function scales accessibility matrices to genomic... |

scaleCorMatrix | This function scales correlation matrices to genomic... |

writeMatrix | Wrapper for making and storing scaled corrleation matrices... |

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