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cff-version: 1.2.0
type: software
title: cooler
message: >-
Please cite this software using the metadata from "preferred-citation".
abstract: >-
Cooler is a Python support library for .cool files: an efficient storage format
for high resolution genomic interaction matrices. The cooler package aims to
provide the following functionality:
* Build contact matrices at any genomic resolution.
* Query contact matrices.
* Export and visualize the data.
* Perform scalable out-of-core operations on the data.
* Provide a clean and well-documented Python API to interact with the data.
Follow cooler development on GitHub.
license: "BSD-3-Clause"
doi: "10.5281/zenodo.597976"
url: "https://open2c.github.io/cooler"
repository-code: "https://github.com/open2c/cooler"
keywords:
- bioinformatics
- genomics
- Hi-C
- sparse
- matrix
- format
- Python
- out-of-core
authors:
- given-names: Nezar
family-names: Abdennur
orcid: "https://orcid.org/0000-0001-5814-0864"
- given-names: Anton
family-names: Goloborodko
orcid: "https://orcid.org/0000-0002-2210-8616"
- given-names: Maxim
family-names: Imakaev
orcid: "https://orcid.org/0000-0002-5320-2728"
- given-names: Peter
family-names: Kerpedjiev
- family-names: Fudenberg
given-names: Geoffrey
orcid: "https://orcid.org/0000-0001-5905-6517"
- family-names: Oullette
given-names: Scott
- given-names: Soohyun
family-names: Lee
orcid: "https://orcid.org/0000-0002-3594-6213"
- given-names: Hendrik
family-names: Strobelt
- given-names: Nils
family-names: Gehlenborg
orcid: "https://orcid.org/0000-0003-0327-8297"
- given-names: Leonid A.
family-names: Mirny
orcid: "https://orcid.org/0000-0002-0785-5410"
preferred-citation:
type: article
title: "Cooler: scalable storage for Hi-C data and other genomically labeled arrays"
authors:
- given-names: Nezar
family-names: Abdennur
orcid: "https://orcid.org/0000-0001-5814-0864"
- given-names: Leonid A.
family-names: Mirny
orcid: "https://orcid.org/0000-0002-0785-5410"
journal: Bioinformatics
month: 1
volume: 36
issue: 1
pages: 311-316
year: 2020
doi: "10.1093/bioinformatics/btz540"
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