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HiCcompare: Joint normalization and comparative analysis of multiple Hi-C datasets

Bioconductor version: Release (3.19)

HiCcompare provides functions for joint normalization and difference detection in multiple Hi-C datasets. HiCcompare operates on processed Hi-C data in the form of chromosome-specific chromatin interaction matrices. It accepts three-column tab-separated text files storing chromatin interaction matrices in a sparse matrix format which are available from several sources. HiCcompare is designed to give the user the ability to perform a comparative analysis on the 3-Dimensional structure of the genomes of cells in different biological states.`HiCcompare` differs from other packages that attempt to compare Hi-C data in that it works on processed data in chromatin interaction matrix format instead of pre-processed sequencing data. In addition, `HiCcompare` provides a non-parametric method for the joint normalization and removal of biases between two Hi-C datasets for the purpose of comparative analysis. `HiCcompare` also provides a simple yet robust method for detecting differences between Hi-C datasets.

Author: Mikhail Dozmorov [aut, cre] , Kellen Cresswell [aut], John Stansfield [aut]

Maintainer: Mikhail Dozmorov <mikhail.dozmorov at>

Citation (from within R, enter citation("HiCcompare")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

HiCcompare Usage Vignette HTML R Script
Reference Manual PDF


biocViews HiC, Normalization, Sequencing, Software
Version 1.26.0
In Bioconductor since BioC 3.6 (R-3.4) (6.5 years)
License MIT + file LICENSE
Depends R (>= 3.5.0), dplyr
Imports data.table, ggplot2, gridExtra, mgcv, stats, InteractionSet, GenomicRanges, IRanges, S4Vectors, BiocParallel, KernSmooth, methods, utils, graphics, pheatmap, gtools, rhdf5
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Suggests knitr, rmarkdown, testthat, multiHiCcompare
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Imports Me multiHiCcompare, SpectralTAD, TADCompare
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Source Package HiCcompare_1.26.0.tar.gz
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macOS Binary (x86_64) HiCcompare_1.26.0.tgz
macOS Binary (arm64) HiCcompare_1.26.0.tgz
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