DOI: 10.18129/B9.bioc.HiCool  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see HiCool.


Bioconductor version: 3.17

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 gmail.com>

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


To install this package, start R (version "4.3") 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:



HTML R Script HiCool
PDF   Reference Manual


biocViews DNA3DStructure, DataImport, HiC, Software
Version 1.0.0
In Bioconductor since BioC 3.17 (R-4.3) (< 6 months)
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
Suggests HiContacts, HiContactsData, AnnotationHub, BiocFileCache, BiocStyle, testthat, knitr, rmarkdown
URL https://github.com/js2264/HiCool
BugReports https://github.com/js2264/HiCool/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package HiCool_1.0.0.tar.gz
Windows Binary
macOS Binary (x86_64) HiCool_1.0.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/HiCool
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/HiCool
Bioc Package Browser https://code.bioconductor.org/browse/HiCool/
Package Short Url https://bioconductor.org/packages/HiCool/
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