Cooler

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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 here or via s3 (bucket s3://cooler01 --endpoint-url https://usgs2.osn.mghpcc.org --no-sign-request).
Many more multires (mcool) files are available on the 4DN data portal.

Installation

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

Citing

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.

@article{cooler2020,
    author = {Abdennur, Nezar and Mirny, Leonid A},
    title = "{Cooler: scalable storage for Hi-C data and other genomically labeled arrays}",
    journal={Bioinformatics},
    volume={36},
    number={1},
    pages={311--316},
    year={2020},
    doi = {10.1093/bioinformatics/btz540},
    url = {https://doi.org/10.1093/bioinformatics/btz540},
}

Contributing

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

Related projects

See other Open2C tools to process Hi-C data (pairtools, distiller) and analyze Hi-C data (cooltools)!
Visualize your cooler data with HiGlass!
Check out this list of 3D genomics tools and papers, most of which accept cooler files.

Affiliations and Acknowledgements

Cooler is an Affiliated Project of NumFOCUS.
Cooler development has received support from the NIH 4D Nucleome Consortium.
We are grateful for a storage allocation from NSF's ACCESS Cyberinfrastucture Open Storage Network to host example cooler data.

Metadata

Release files for cooler 0.10.4

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for cooler 0.10.4
File	Size	Uploaded
cooler-0.10.4.tar.gz	11.1 MB	Jul 21, 2025	Details

Built distribution (wheel)

Table of built distributions (wheels) for cooler 0.10.4
File	Interpreter	ABI	Platform	Reset
cooler-0.10.4-py3-none-any.whl 109.3 kB Jul 21, 2025	Python 3	none	any	Details

Total release size: 11.2 MB

Release files / cooler-0.10.4.tar.gz

Download URL	cooler-0.10.4.tar.gz
Size	11.1 MB
Tags	Source
SHA-256 checksum How to use checksums	`1c25626d5970cedd1ff651966c36d97073a697a7830d369b43b2d0e59ce405ba`
BLAKE2b-256 checksum How to use checksums	`64762527cef69c2f71f18341be4e29e017bfe2af054afe8b2d106465391fc51e`
Upload date	Jul 21, 2025
Uploaded using Trusted Publishing? What is trusted publishing?	Yes
Uploaded via	`twine/6.1.0 CPython/3.12.9`

Provenance

Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.

Identity

Publishing platform: GitHub Actions
Publishing repository: github.com/open2c/cooler
Publishing commit: github.com/open2c/cooler/tree/a981796113e3045267b600537ede7617629196ca

Workflow

Publishing configuration: github.com/open2c/cooler/blob/a981796113e3045267b600537ede7617629196ca/.github/workflows/publish.yml
Publishing logs: github.com/open2c/cooler/actions/runs/16430866735/attempts/1

Artifact

Subject: cooler-0.10.4.tar.gz
SHA-256 checksum: 1c25626d5970cedd1ff651966c36d97073a697a7830d369b43b2d0e59ce405ba Verifying attestations

Release files / cooler-0.10.4-py3-none-any.whl

Download URL	cooler-0.10.4-py3-none-any.whl
Size	109.3 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`f245de63d05cd9e25961f85a8226929faa3607575be38dd5b6e33a200cef319e`
BLAKE2b-256 checksum How to use checksums	`0c1a0725a7037a69968ec3e6573f0bdc2fab1d9976c114618e2a2032ba0af66c`
Upload date	Jul 21, 2025
Uploaded using Trusted Publishing? What is trusted publishing?	Yes
Uploaded via	`twine/6.1.0 CPython/3.12.9`

Provenance

Identity

Publishing platform: GitHub Actions
Publishing repository: github.com/open2c/cooler
Publishing commit: github.com/open2c/cooler/tree/a981796113e3045267b600537ede7617629196ca

Workflow

Publishing configuration: github.com/open2c/cooler/blob/a981796113e3045267b600537ede7617629196ca/.github/workflows/publish.yml
Publishing logs: github.com/open2c/cooler/actions/runs/16430866735/attempts/1

Artifact

Subject: cooler-0.10.4-py3-none-any.whl
SHA-256 checksum: f245de63d05cd9e25961f85a8226929faa3607575be38dd5b6e33a200cef319e Verifying attestations