Irreproducible Discovery Rate for Genomic Interactions Data

calculate_midpoint_distance1d | Distance between Midpoints of two Peaks |

calculate_midpoint_distance2d | Distance between Anchor Midpoints of two Interactions |

calculate_relative_overlap1d | Relative Anchor Overlap of two Peaks |

calculate_relative_overlap2d | Relative Anchor Overlap of two Interactions |

chiapet | Example Genomic Interaction Data Set |

chipseq | Example Genomic Peak Data Set |

determine_anchor_overlap | Identifies Overlapping Anchors |

draw_hic_contact_map | Create Hi-C contact map |

draw_idr_distribution_histogram | Create histogram of IDR values |

draw_rank_idr_scatterplot | Create scatterplot of IDR values |

draw_value_idr_scatterplot | Create scatterplot of IDR values |

establish_bijection | Finds One-to-One Correspondence between Peaks or interactions... |

establish_bijection1d | Finds One-to-One Correspondence between Peaks from Replicate... |

establish_bijection2d | Finds One-to-One Correspondence between Interactions from... |

establish_overlap1d | Establish m:n Mapping Between Peaks from Replicate 1 and 2 |

establish_overlap2d | Establish m:n mapping between interactions from replicate 1... |

estimate_idr | Estimates IDR for Genomic Peaks or Genomic Interactions |

estimate_idr1d | Estimates IDR for Genomic Peak Data |

estimate_idr2d | Estimates IDR for Genomic Interaction Data |

estimate_idr2d_hic | Estimates IDR for Genomic Interactions measured by Hi-C... |

hic | Example Hi-C data set |

parse_hic_pro_matrix | Parse .matrix and .bed files from HiC-Pro for IDR2D analysis |

parse_juicer_matrix | Parse .hic files from Juicer for IDR2D analysis |

preprocess | Prepares Data for IDR Analysis |

remove_nonstandard_chromosomes1d | Removes Peaks on Non-standard Chromosomes |

remove_nonstandard_chromosomes2d | Removes Interactions on Non-standard Chromosomes |

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