Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs

addCor | Add correlation of ChIP-seq coverage to motif pairs. |

addCovCor | Add correlation of anchor signals to pairs of close genomic... |

addCovToGR | Add coverage to regions in 'GRanges' object. |

addInteractionSupport | Add column to 'GInteractions' with overlap support. |

addMotifScore | Add motif score of anchors. |

addStrandCombination | Add combination of anchor strand orientation. |

cutoffBest10 | Default optimal cutoff value of logistic regression. |

cutoffByTF | Optimal cutoff values for logistic regression models. |

getCisPairs | Build a 'GInteractions' object with all pairs of input... |

getOutOfBound | Get out of chromosomal bound ranges. |

modelBest10Avg | Default parameters for logistic regression model in sevenC. |

motif.hg19.CTCF | CTCF motif locations in human genome hg19. |

motif.hg19.CTCF.chr22 | CTCF motif locations on chromosome 22 in human genome hg19. |

motif.hg19.CTCF.chr22.cov | CTCF motifs on human chromosome 22 with example coverage. |

noZeroVar | returns indices of columns with non-zero variance |

parseLoopsRao | Parse chromatin loops from Rao et al. 2014 as strict... |

parseLoopsTang | Parse chromatin interactions from Tang et al. 2015 as... |

predLogit | Predict interaction probability using logistic regression... |

predLoops | Predict looping interactions. |

prepareCisPairs | Prepares motif pairs as 'GInteractions' and add genomic... |

sevenC | Computational chromosome conformation capture by correlation... |

slideMean | Sliding mean over x of intervals of size k |

TFspecificModels | TF specific parameters for logistic regression in sevenC |

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.