{"id":27645926,"url":"https://github.com/open2c/cooler","last_synced_at":"2025-05-15T09:08:19.574Z","repository":{"id":43057264,"uuid":"49553222","full_name":"open2c/cooler","owner":"open2c","description":"A cool place to store your 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Cooler\n\n\u003ca href=\"https://open2c.github.io/cooler\"\u003e\u003cimg width=\"25%\" src=\"https://github.com/open2c/cooler/raw/master/docs/cooler_logo.png\" alt=\"Cooler\"\u003e\u003c/a\u003e\n\n\u003ctable\u003e\n    \u003ctr\u003e\n        \u003ctd\u003eLatest Release\u003c/td\u003e\n        \u003ctd\u003e\n            \u003ca href=\"https://pypi.org/project/cooler/\"\u003e\n                \u003cimg src=\"https://img.shields.io/pypi/v/cooler?color=blue\u0026label=PyPI%20package\" alt=\"latest release pypi\"\u003e\n            \u003c/a\u003e\n            \u003ca href=\"https://bioconda.github.io/recipes/cooler/README.html\"\u003e\n                \u003cimg src=\"https://img.shields.io/conda/vn/bioconda/cooler?color=blue\" alt=\"latest release bioconda\"\u003e\n            \u003c/a\u003e\n        \u003c/td\u003e\n    \u003c/tr\u003e\n    \u003ctr\u003e\n        \u003ctd\u003eLicense\u003c/td\u003e\n        \u003ctd\u003e\n            \u003ca href=\"https://github.com/open2c/cooler/blob/master/LICENSE\"\u003e\n                \u003cimg src=\"https://img.shields.io/badge/license-BSD-green\" alt=\"license\"\u003e\n                \u003c!-- \u003cimg src=\"https://img.shields.io/pypi/l/cooler.svg\" alt=\"license\"\u003e --\u003e\n            \u003c/a\u003e\n        \u003c/td\u003e\n    \u003c/tr\u003e\n    \u003ctr\u003e\n        \u003ctd\u003eBuild Status\u003c/td\u003e\n        \u003ctd\u003e\n            \u003ca href=\"https://github.com/open2c/cooler/blob/master/.github/workflows/ci.yml\"\u003e\n                \u003cimg src=\"https://github.com/open2c/cooler/actions/workflows/ci.yml/badge.svg\" alt=\"build status\"\u003e\n            \u003c/a\u003e\n        \u003c/td\u003e\n    \u003c/tr\u003e\n    \u003ctr\u003e\n      \u003ctd\u003ePre-commit Status\u003c/td\u003e\n      \u003ctd\u003e\n        \u003ca href=\"https://results.pre-commit.ci/repo/github/49553222\"\u003e\n        \u003cimg src=\"https://results.pre-commit.ci/badge/github/open2c/cooler/master.svg\" alt=\"pre-commit status\" /\u003e\n        \u003c/a\u003e\n      \u003c/td\u003e\n    \u003c/tr\u003e\n    \u003ctr\u003e\n        \u003ctd\u003eDocs Status\u003c/td\u003e\n        \u003ctd\u003e\n            \u003ca href=\"http://cooler.readthedocs.org/en/latest/\"\u003e\n                \u003cimg src=\"https://readthedocs.org/projects/cooler/badge/?version=latest\"\u003e\n            \u003c/a\u003e\n        \u003c/td\u003e\n    \u003c/tr\u003e\n    \u003ctr\u003e\n        \u003ctd\u003eCoverage\u003c/td\u003e\n        \u003ctd\u003e\n            \u003ca href=\"https://codecov.io/gh/open2c/cooler\"\u003e\n                \u003cimg src=\"https://codecov.io/gh/open2c/cooler/branch/master/graph/badge.svg\" alt=\"coverage\"\u003e\n            \u003c/a\u003e\n        \u003c/td\u003e\n    \u003c/tr\u003e\n    \u003ctr\u003e\n        \u003ctd\u003eDownloads\u003c/td\u003e\n        \u003ctd\u003e\n            \u003ca href=\"https://pypi.org/project/cooler\"\u003e\n                \u003cimg src=\"https://static.pepy.tech/personalized-badge/cooler?period=total\u0026units=international_system\u0026left_color=grey\u0026right_color=blue\u0026left_text=PyPI%20downloads\" alt=\"pypi downloads\"\u003e\n            \u003c/a\u003e\n            \u003ca href=\"http://bioconda.github.io/recipes/cooler/README.html\"\u003e\n                \u003cimg src=\"https://img.shields.io/conda/dn/bioconda/cooler.svg?style=flat\u0026label=Bioconda downloads\" alt=\"bioconda downloads\"\u003e\n            \u003c/a\u003e\n        \u003c/td\u003e\n    \u003c/tr\u003e\n    \u003ctr\u003e\n        \u003ctd\u003eCitation\u003c/td\u003e\n        \u003ctd\u003e\n            \u003ca href=\"https://doi.org/10.1093/bioinformatics/btz540\"\u003e\n                \u003cimg src=\"https://img.shields.io/badge/DOI-10.1093%2Fbioinformatics%2Fbtz540-blue\" alt=\"paper doi\"\u003e\n            \u003c/a\u003e\n            \u003ca href=\"https://zenodo.org/badge/latestdoi/49553222\"\u003e\n                \u003cimg src=\"https://zenodo.org/badge/49553222.svg\" alt=\"zenodo doi\"\u003e\n            \u003c/a\u003e\n        \u003c/td\u003e\n    \u003c/tr\u003e\n    \u003ctr\u003e\n        \u003ctd\u003eCommunity\u003c/td\u003e\n        \u003ctd\u003e\n            \u003ca href=\"https://bit.ly/open2c-slack\"\u003e\n                \u003cimg src=\"https://img.shields.io/badge/chat-slack-%233F0F3F?logo=slack\" alt=\"slack\"\u003e\n            \u003c/a\u003e\n            \u003ca href=\"https://www.numfocus.org/\"\u003e\n                \u003cimg src=\"https://img.shields.io/badge/powered%20by-NumFOCUS-orange.svg?style=flat\u0026colorA=E1523D\u0026colorB=007D8A\" alt=\"numfocus\"\u003e\n            \u003c/a\u003e\n        \u003c/td\u003e\n    \u003c/tr\u003e\n\u003c/table\u003e\n\n## A cool place to store your Hi-C\n\nCooler is a support library for a **sparse, compressed, binary** persistent storage [format](http://cooler.readthedocs.io/en/latest/schema.html), also called cooler, used to store genomic interaction data, such as Hi-C contact matrices.\n\nThe cooler file format is an implementation of a genomic matrix data model using [HDF5](https://en.wikipedia.org/wiki/Hierarchical_Data_Format) as the container format. The `cooler` package includes a suite of [command line tools](http://cooler.readthedocs.io/en/latest/cli.html) and a [Python API](http://cooler.readthedocs.io/en/latest/api.html) to facilitate creating, querying and manipulating cooler files.\n\nTo get started:\n\n- [Install](#Installation) cooler\n- Read the [documentation](http://cooler.readthedocs.org/en/stable/) and see the Jupyter Notebook [walkthrough](https://github.com/open2c/cooler-binder).\n- _cool_ files from published Hi-C data sets are available [here](https://usgs2.osn.mghpcc.org/cooler01/index.html) or via s3 (bucket `s3://cooler01 --endpoint-url https://usgs2.osn.mghpcc.org --no-sign-request`).\n- Many more multires (_mcool_) files are available on the [4DN data portal](https://data.4dnucleome.org/visualization/index).\n\n### Installation\n\nInstall from PyPI using pip.\n```sh\n$ pip install cooler\n```\n\nIf you are using `conda`, you can alternatively install `cooler` from the [bioconda](https://bioconda.github.io/index.html) channel.\n```sh\n$ conda install -c conda-forge -c bioconda cooler\n```\n\n### Citing\n\nAbdennur, N., and Mirny, L.A. (2020). Cooler: scalable storage for Hi-C data and other genomically labeled arrays. _Bioinformatics_. doi: [10.1093/bioinformatics/btz540](https://doi.org/10.1093/bioinformatics/btz540).\n\n```bibtex\n@article{cooler2020,\n    author = {Abdennur, Nezar and Mirny, Leonid A},\n    title = \"{Cooler: scalable storage for Hi-C data and other genomically labeled arrays}\",\n    journal={Bioinformatics},\n    volume={36},\n    number={1},\n    pages={311--316},\n    year={2020},\n    doi = {10.1093/bioinformatics/btz540},\n    url = {https://doi.org/10.1093/bioinformatics/btz540},\n}\n```\n\n### Contributing\n\nInterested in contributing to cooler? That's great! To get started, check out the [contributing guide](https://github.com/open2c/cooler/blob/master/CONTRIBUTING.md).\n\n\n### Related projects\n\n- See other Open2C tools to process Hi-C data ([pairtools](https://github.com/open2c/pairtools), [distiller](https://github.com/open2c/distiller-nf)) and analyze Hi-C data ([cooltools](https://github.com/open2c/cooltools))!\n- Visualize your cooler data with [HiGlass](http://higlass.io)!\n- Check out this list of [3D genomics tools and papers](https://github.com/mdozmorov/HiC_tools), most of which accept cooler files.\n\n### Affiliations and Acknowledgements\n\n* Cooler is an Affiliated Project of [NumFOCUS](https://www.numfocus.org/).\n* Cooler development has received support from the NIH [4D Nucleome](https://www.4dnucleome.org/) Consortium.\n* We are grateful for a storage allocation from NSF's [ACCESS Cyberinfrastucture](https://access-ci.org/) Open Storage Network to host example cooler data.\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fopen2c%2Fcooler","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fopen2c%2Fcooler","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fopen2c%2Fcooler/lists"}