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Bioconductor class for interacting with Hi-C files in R

Bioconductor version: Release (3.19)

R generic interface to Hi-C contact matrices in `.(m)cool`, `.hic` or HiC-Pro derived formats, as well as other Hi-C processed file formats. Contact matrices can be partially parsed using a random access method, allowing a memory-efficient representation of Hi-C data in R. The `HiCExperiment` class stores the Hi-C contacts parsed from local contact matrix files. `HiCExperiment` instances can be further investigated in R using the `HiContacts` analysis package.

Author: Jacques Serizay [aut, cre]

Maintainer: Jacques Serizay <jacquesserizay at>

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


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:

Introduction to HiCExperiment HTML R Script
Reference Manual PDF


biocViews DNA3DStructure, DataImport, HiC, Software
Version 1.4.0
In Bioconductor since BioC 3.17 (R-4.3) (1 year)
License MIT + file LICENSE
Depends R (>= 4.2)
Imports InteractionSet, strawr, GenomeInfoDb, GenomicRanges, IRanges, S4Vectors, BiocGenerics, BiocIO, BiocParallel, methods, rhdf5, Matrix, vroom, dplyr, stats
System Requirements
Bug Reports
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Suggests HiContacts, HiContactsData, BiocFileCache, rtracklayer, testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown
Linking To
Depends On Me HiContacts, HiCool, DNAZooData
Imports Me fourDNData, OHCA
Suggests Me
Links To Me
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package HiCExperiment_1.4.0.tar.gz
Windows Binary
macOS Binary (x86_64) HiCExperiment_1.4.0.tgz
macOS Binary (arm64) HiCExperiment_1.4.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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