DOI: 10.18129/B9.bioc.HiCExperiment  

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

Bioconductor class for interacting with Hi-C files in R

Bioconductor version: Development (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 gmail.com>

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


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:



HTML R Script Introduction to HiCExperiment
PDF   Reference Manual


biocViews DNA3DStructure, DataImport, HiC, Software
Version 1.3.0
In Bioconductor since BioC 3.17 (R-4.3) (0.5 years)
License MIT + file LICENSE
Depends R (>= 4.2)
Imports InteractionSet, strawr, GenomeInfoDb, GenomicRanges, IRanges, S4Vectors, BiocGenerics, BiocIO, BiocParallel, methods, rhdf5, Matrix, vroom, dplyr, stats
Suggests HiContacts, HiContactsData, BiocFileCache, rtracklayer, testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown
URL https://github.com/js2264/HiCExperiment
BugReports https://github.com/js2264/HiCExperiment/issues
Depends On Me DNAZooData, HiContacts, HiCool
Imports Me fourDNData
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package HiCExperiment_1.3.0.tar.gz
Windows Binary HiCExperiment_1.3.0.zip
macOS Binary (x86_64) HiCExperiment_1.3.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/HiCExperiment
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/HiCExperiment
Bioc Package Browser https://code.bioconductor.org/browse/HiCExperiment/
Package Short Url https://bioconductor.org/packages/HiCExperiment/
Package Downloads Report Download Stats

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