Skip to main content

Sparse binary format for genomic interaction matrices.

Project description



Latest Release latest release pypi latest release bioconda
License license
Build Status build status
Pre-commit Status pre-commit status
Docs Status
Coverage coverage
Downloads pypi downloads bioconda downloads
Citation paper doi zenodo doi
Community slack

A cool place to store your Hi-C

Cooler is a support library for a sparse, compressed, binary persistent storage format, also called cooler, used to store genomic interaction data, such as Hi-C contact matrices.

The cooler file format is an implementation of a genomic matrix data model using HDF5 as the container format. The cooler package includes a suite of command line tools and a Python API to facilitate creating, querying and manipulating cooler files.

To get started:

  • Install cooler
  • Read the documentation and see the Jupyter Notebook walkthrough.
  • cool files from published Hi-C data sets are available at
  • Many more multires (mcool) files are available on the 4DN data portal.


Install from PyPI using pip.

$ pip install cooler

If you are using conda, you can alternatively install cooler from the bioconda channel.

$ conda install -c conda-forge -c bioconda cooler


Abdennur, N., and Mirny, L.A. (2020). Cooler: scalable storage for Hi-C data and other genomically labeled arrays. Bioinformatics. doi: 10.1093/bioinformatics/btz540.

    author = {Abdennur, Nezar and Mirny, Leonid A},
    title = "{Cooler: scalable storage for Hi-C data and other genomically labeled arrays}",
    doi = {10.1093/bioinformatics/btz540},
    url = {},


Interested in contributing to cooler? That's great! To get started, check out the contributing guide.

Related projects

Project details

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

cooler-0.9.3.tar.gz (11.1 MB view hashes)

Uploaded source

Built Distribution

cooler-0.9.3-py3-none-any.whl (103.7 kB view hashes)

Uploaded py3

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page