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.