Cooler file format

Abbreviation: .cool

General Information

Cooler is a file format that implements genomically-labeled sparse 2D arrays (matrices) with identical axes in HDF5. It is also the name of the Python package that supports the format. Cooler was designed for the storage and manipulation of extremely large Hi-C datasets at any resolution, but is not limited to Hi-C data in any way. Standard file extensions are .cool for single-resolution cooler files and .mcool for files storing multiple resolutions.

Homepage https://cooler.readthedocs.io/en/latest/datamodel.html

Countries that developed this resource United States

Created in 2016

Taxonomic range

All

Knowledge Domains

Subjects

User-defined Tags

Chromosome Conformation

Genomic Contacts

Hi-C

How to cite this record FAIRsharing.org: .cool; Cooler file format; DOI: https://doi.org/10.25504/FAIRsharing.VJDEtl; Last edited: Sept. 20, 2019, 11:52 a.m.; Last accessed: Oct 20 2019 6:20 p.m.

Publication for citation Cooler: scalable storage for Hi-C data and other genomically-labeled arrays Abdennur, N and Mirny, L; bioRxiv ; 2019.

This record is maintained by 4DNucleome DCIC (4dn_dcic)

Record added: April 24, 2019, 4:37 p.m.
Record updated: April 29, 2019, 9:32 a.m. by The FAIRsharing Team.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.VJDEtl' by 'The FAIRsharing Team' at 09:32, 29 Apr 2019 (not approved):

	'supportLinks' has been modified:
		Before:
			online documentation|https://cooler.readthedocs.io/en/latest/index.html
		After:
			forum|https://github.com/mirnylab/cooler/issues
			online documentation|https://cooler.readthedocs.io/en/latest/index.html
			online documentation|https://github.com/mirnylab/cooler
		Added:
			forum|https://github.com/mirnylab/cooler/issues
			online documentation|https://github.com/mirnylab/cooler
		Removed:

	'licences' has been modified:
		Before:
		After:
			BSD-3-Clause License (Modified BSD License) (New BSD License)|https://opensource.org/licenses/BSD-3-Clause|Data
		Added:
			BSD-3-Clause License (Modified BSD License) (New BSD License)|https://opensource.org/licenses/BSD-3-Clause|Data
		Removed:

	'onto_domains' has been modified:
		Before:
		After:
			chromosome
		Added:
			chromosome
		Removed:

	'related_standards' has been modified:
		Before:
			Pairs file format
		After:
			Pairs file format
			Hierarchical Data Format (HDF)
		Added:
			Hierarchical Data Format (HDF)
		Removed:

	'taxonomies' has been modified:
		Before:
			Not applicable
		After:
			All
		Added:
			All
		Removed:
			Not applicable

	'homepage' has been modified:
		Before: https://cooler.readthedocs.io/en/latest/
		After: https://cooler.readthedocs.io/en/latest/datamodel.html

Support

General

forum	GitHub Issue Tracker
online documentation	Documentation
online documentation	GitHub Repository

Additional Information

Contact

Nezar Abdennur ORCID

Tools

Cooler	https://mirnylab.github.io/cooler/	0.8.5
4DN Hi-C Processing Pipeline (Docker image)	https://hub.docker.com/r/duplexa/4dn-hic/	v43
HiGlass	https://higlass.io/	1.5

Schemas

No XSD schemas defined

Access / Retrieve Data

Conditions of Use

Applies to: Data use

BSD-3-Clause License (Modified BSD License) (New BSD License)

Publications

Cooler: scalable storage for Hi-C data and other genomically-labeled arrays

Abdennur, N and Mirny, L
bioRxiv 2019

Link to Publication

Related Standards

Reporting Guidelines

No guidelines defined

Terminology Artifacts

No semantic standards defined

Models and Formats

Identifier Schemas

No identifier schema standards defined

Metrics

No metrics standards defined

Implementing Databases (1)

4DNucleome Data Portal
The 4D Nucleome Data Portal (4DN) hosts data generated by the 4DN Network and other reference nucleomics data sets, and an expanding tool set for open data processing and visualization. It is a platform to search, visualize, and download nucleomics data.

Implementing Policies

This record is not implemented by any policy.

Credit

Record Maintainer

This record is maintained by 4DNucleome DCIC (4dn_dcic)

Funds

NIH Common Fund, USA (Government body)

Maintains

Mirny Lab (Lab) Lead

Grant Number(s)

U54-DK107980-01 (NIH Common Fund, USA)

Cooler file format

We need your help!

Developed by

Contact Us

About FAIRsharing