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


Bioconductor version: Development (3.20)

HiCool provides an R interface to process and normalize Hi-C paired-end fastq reads into .(m)cool files. .(m)cool is a compact, indexed HDF5 file format specifically tailored for efficiently storing HiC-based data. On top of processing fastq reads, HiCool provides a convenient reporting function to generate shareable reports summarizing Hi-C experiments and including quality controls.

Author: Jacques Serizay [aut, cre]

Maintainer: Jacques Serizay <jacquesserizay at>

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


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:

HiCool HTML R Script
Reference Manual PDF


biocViews DNA3DStructure, DataImport, HiC, Software
Version 1.5.0
In Bioconductor since BioC 3.17 (R-4.3) (1 year)
License MIT + file LICENSE
Depends R (>= 4.2), HiCExperiment
Imports BiocIO, S4Vectors, GenomicRanges, IRanges, InteractionSet, vroom, basilisk, reticulate, rmarkdown, rmdformats, plotly, dplyr, stringr, sessioninfo, utils
System Requirements
Bug Reports
See More
Suggests HiContacts, HiContactsData, AnnotationHub, BiocFileCache, BiocStyle, testthat, knitr, rmarkdown
Linking To
Depends On Me
Imports Me OHCA
Suggests Me
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Build Report Build Report

Package Archives

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

Source Package HiCool_1.5.0.tar.gz
Windows Binary
macOS Binary (x86_64) HiCool_1.5.0.tgz
macOS Binary (arm64)
Source Repository git clone
Source Repository (Developer Access) git clone
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