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This is the development version of multiHiCcompare; for the stable release version, see multiHiCcompare.

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

Bioconductor version: Development (3.20)

multiHiCcompare provides functions for joint normalization and difference detection in multiple Hi-C datasets. This extension of the original HiCcompare package now allows for Hi-C experiments with more than 2 groups and multiple samples per group. multiHiCcompare operates on processed Hi-C data in the form of sparse upper triangular matrices. It accepts four column (chromosome, region1, region2, IF) tab-separated text files storing chromatin interaction matrices. multiHiCcompare provides cyclic loess and fast loess (fastlo) methods adapted to jointly normalizing Hi-C data. Additionally, it provides a general linear model (GLM) framework adapting the edgeR package to detect differences in Hi-C data in a distance dependent manner.

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

Maintainer: Mikhail Dozmorov <mikhail.dozmorov at>

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


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

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

# The following initializes usage of Bioc devel


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:

juiceboxVisualization HTML R Script
multiHiCcompare HTML R Script
Reference Manual PDF


biocViews HiC, Normalization, Sequencing, Software
Version 1.23.0
In Bioconductor since BioC 3.8 (R-3.5) (5.5 years)
License MIT + file LICENSE
Depends R (>= 4.0.0)
Imports data.table, dplyr, HiCcompare, edgeR, BiocParallel, qqman, pheatmap, methods, GenomicRanges, graphics, stats, utils, pbapply, GenomeInfoDbData, GenomeInfoDb, aggregation
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Suggests knitr, rmarkdown, testthat, BiocStyle
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Imports Me HiCDOC, OHCA
Suggests Me HiCcompare
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Source Package multiHiCcompare_1.23.0.tar.gz
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