Normalize and detect differences between Hi-C datasets when replicates of each experimental condition are available

cyclic_loess | Cyclic Loess normalization for Hi-C data |

exportJuicebox | Export multiHiCcompare results for visualization in Juicebox |

fastlo | Perform fast loess normalization on a Hi-C experiment |

HCT116_r1 | A 4 column sparse matrix for a Hi-C matrix. |

HCT116_r2 | A 4 column sparse matrix for a Hi-C matrix. |

HCT116_r3 | A 4 column sparse matrix for a Hi-C matrix. |

HCT116_r4 | A 4 column sparse matrix for a Hi-C matrix. |

HCT116_r5 | A 4 column sparse matrix for a Hi-C matrix. |

HCT116_r6 | A 4 column sparse matrix for a Hi-C matrix. |

hg19_cyto | A GenomicRanges object containing centromeric, gvar, and... |

hg38_cyto | A GenomicRanges object containing centromeric, gvar, and... |

hic_exactTest | Perform exact test based difference detection on a Hi-C... |

hicexp2 | hicexp object with 4 samples from two groups. |

Hicexp-class | An S4 class for working with Hi-C data |

hicexp_diff | hicexp object with 7 samples from two groups. |

hic_filter | Perform filtering on a Hi-C experiment |

hic_glm | Function to perform GLM differential analysis on Hi-C... |

hic_scale | Perform library scaling on a hicexp object |

hic_table | Print the hic_table |

make_hicexp | Make Hi-C experiment object from data |

manhattan_hicexp | Manhattan plot function for results of multiHiCcompare |

MD_composite | Plot a composite MD plot with the results of a comparison |

MD_hicexp | Make MD plots for all combinations of a condition |

meta | Print the metadata |

normalized | Print the indicator for if the data is normalized |

perm_test | Perform a permutation test to check enrichment of a genomic... |

plot_counts | Plot the count results from topDirs |

plot_pvals | Plot the p-value results from topDirs |

pval_heatmap | Function to visualize p-values from multiHiCcompare results |

resolution | Print the resolution |

results | Print the results |

show | Print information about a HiCexp object |

smartApply | Function to apply either biocParallel or standard lapply |

topDirs | Filter results of multiHiCcompare |

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