Metadata-Version: 2.1
Name: cooler
Version: 0.8.10
Summary: Sparse binary format for genomic interaction matrices
Home-page: https://github.com/mirnylab/cooler
Author: Nezar Abdennur
Author-email: nezar@mit.edu
License: BSD
Description: # Cooler
        
        <a href="https://mirnylab.github.io/cooler"><img width="25%" src="https://github.com/mirnylab/cooler/raw/master/docs/cooler_logo.png" alt="Cooler"></a>
        
        [![Build Status](https://travis-ci.org/mirnylab/cooler.svg?branch=master)](https://travis-ci.org/mirnylab/cooler)
        [![CodeCov](https://codecov.io/gh/mirnylab/cooler/branch/master/graph/badge.svg)](https://codecov.io/gh/mirnylab/cooler)
        [![Documentation Status](https://readthedocs.org/projects/cooler/badge/?version=latest)](http://cooler.readthedocs.org/en/latest/)
        [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-square)](http://bioconda.github.io/recipes/cooler/README.html)
        [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/mirnylab/cooler-binder/master)
        [![Join the chat at https://gitter.im/mirnylab/cooler](https://badges.gitter.im/mirnylab/cooler.svg)](https://gitter.im/mirnylab/cooler?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
        [![DOI](https://zenodo.org/badge/49553222.svg)](https://zenodo.org/badge/latestdoi/49553222)
        
        ## A cool place to store your Hi-C
        
        Cooler 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.
        
        The 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.
        
        To get started:
        
        - [Install](#Installation) cooler
        - Read the [documentation](http://cooler.readthedocs.org/en/latest/) and see the Jupyter Notebook [walkthrough](https://github.com/mirnylab/cooler-binder).
        - _cool_ files from published Hi-C data sets are available at `ftp://cooler.csail.mit.edu/coolers`.
        - Many more multires (_mcool_) files are available on the [4DN data portal](https://data.4dnucleome.org/visualization/index).
        
        ### Installation
        
        Install from PyPI using pip.
        ```sh
        $ pip install cooler
        ```
        
        If you are using `conda`, you can alternatively install `cooler` from the [bioconda](https://bioconda.github.io/index.html) channel.
        ```sh
        $ conda install -c conda-forge -c bioconda cooler
        ```
        
        Requirements:
        
        - Python 2.7/3.4+
        - libhdf5 and Python packages `numpy`, `scipy`, `pandas`, `h5py`. We highly recommend using the `conda` package manager to install scientific packages like these. To get it, you can either install the full [Anaconda](https://www.continuum.io/downloads) Python distribution or just the standalone [conda](http://conda.pydata.org/miniconda.html) package manager.
        
        See the [docs](http://cooler.readthedocs.org/en/latest/) for more information.
        
        **NOTE: Python 2.7 support will sunset with cooler 0.8.**
        
        
        ### Contributing
        
        Interested in contributing to cooler? That's great! To get started, check out the [contributing guide](https://github.com/mirnylab/cooler/blob/master/CONTRIBUTING.md).
        
        
        ### Citing
        
        Abdennur, N., and Mirny, L. (2019). 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).
        
        ```bibtex
        @article{Cooler2019,
            author = {Abdennur, Nezar and Mirny, Leonid A},
            title = "{Cooler: scalable storage for Hi-C data and other genomically labeled arrays}",
            journal = {Bioinformatics},
            year = {2019},
            month = {07},
            doi = {10.1093/bioinformatics/btz540},
            url = {https://doi.org/10.1093/bioinformatics/btz540},
        }
        ```
        
        ### License
        
        BSD (3 Clause)
        
        ### Related projects
        
        - Process Hi-C data with [distiller](https://github.com/mirnylab/distiller)!
        - Downstream analysis with [cooltools](https://github.com/mirnylab/cooltools)!
        - Visualize your cooler data with [HiGlass](http://higlass.io)!
        
        
Keywords: genomics,bioinformatics,Hi-C,contact,matrix,format,hdf5
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Description-Content-Type: text/markdown
Provides-Extra: tests
Provides-Extra: docs
Provides-Extra: all
