cooler

A cool place to store your Hi-C

https://github.com/open2c/cooler

Science Score: 77.0%

This score indicates how likely this project is to be science-related based on various indicators:

✓
CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
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DOI references
Found 8 DOI reference(s) in README
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Academic publication links
Links to: zenodo.org
✓
Committers with academic emails
2 of 19 committers (10.5%) from academic institutions
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (9.9%) to scientific vocabulary

Keywords

3d-genome bioinformatics chromatin contact-matrix cooler file-format genomics hdf5 hi-c ngs python sparse

Keywords from Contributors

interaction cython optim notebooks mesh molecular-dynamics-simulation yolov5s hydrology pdes regionalization

Last synced: 4 months ago · JSON representation ·

Repository

A cool place to store your Hi-C

Basic Info

Host: GitHub
Owner: open2c
License: bsd-3-clause
Language: Python
Default Branch: master
Homepage: https://open2c.github.io/cooler
Size: 88.3 MB

Statistics

Stars: 223
Watchers: 14
Forks: 59
Open Issues: 49
Releases: 46

Topics

3d-genome bioinformatics chromatin contact-matrix cooler file-format genomics hdf5 hi-c ngs python sparse

Created almost 10 years ago · Last pushed 5 months ago

Metadata Files

Readme Changelog Contributing License Citation

Cooler

Latest Release
License
Build Status
Pre-commit Status
Docs Status
Coverage
Downloads
Citation
Community

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. sh $ pip install cooler

If you are using conda, you can alternatively install cooler from the bioconda channel. sh $ 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.

bibtex @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.

Owner

Name: Open Chromosome Collective
Login: open2c
Kind: organization
Email: open.chromosome.collective@gmail.com

Website: https://open2c.github.io/
Repositories: 14
Profile: https://github.com/open2c

Citation (CITATION.cff)

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"

GitHub Events

Total

Create event: 3
Release event: 2
Issues event: 20
Watch event: 16
Issue comment event: 47
Push event: 40
Pull request review event: 8
Pull request review comment event: 9
Pull request event: 19
Fork event: 7

Last Year

Create event: 3
Release event: 2
Issues event: 20
Watch event: 16
Issue comment event: 47
Push event: 40
Pull request review event: 8
Pull request review comment event: 9
Pull request event: 19
Fork event: 7

Committers

Last synced: 8 months ago

All Time

Total Commits: 980
Total Committers: 19
Avg Commits per committer: 51.579
Development Distribution Score (DDS): 0.156

Past Year

Commits: 27
Committers: 4
Avg Commits per committer: 6.75
Development Distribution Score (DDS): 0.444

Top Committers

Name	Email	Commits
Nezar	n**r@g**m	827
Peter Kerpedjiev	p**v@g**m	39
pre-commit-ci[bot]	6****]	29
Joachim Wolff	w**j@i**e	20
Anton Goloborodko	g**n@g**m	10
Phlya	f**r@g**m	9
Thomas Reimonn	t**n@u**u	9
gfudenberg	g**g@g**m	8
Roberto Rossini	7****s	7
cc3065	t**t@t**t	4
Leon Rauschning	9****g	4
Garrett Ng	5****g	4
dependabot[bot]	4****]	3
Maksim Imakaev	m**v@g**m	2
Cyril Matthey-Doret	c**t@u**h	1
Alexandre Detiste	a**e@g**m	1
Scott Ouellette	s****x	1
The Gitter Badger	b**r@g**m	1
Trevor Manz	t**z@g**m	1

Committer Domains (Top 20 + Academic)

gitter.im: 1 unil.ch: 1 test.test: 1 umassmed.edu: 1 informatik.uni-freiburg.de: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time

Total issues: 49
Total pull requests: 59
Average time to close issues: about 1 month
Average time to close pull requests: 23 days
Total issue authors: 41
Total pull request authors: 15
Average comments per issue: 1.9
Average comments per pull request: 0.47
Merged pull requests: 40
Bot issues: 0
Bot pull requests: 24

Past Year

Issues: 16
Pull requests: 19
Average time to close issues: 5 days
Average time to close pull requests: 15 days
Issue authors: 15
Pull request authors: 9
Average comments per issue: 1.75
Average comments per pull request: 0.68
Merged pull requests: 3
Bot issues: 0
Bot pull requests: 2

View more stats

Top Authors

Issue Authors

nvictus (4)
BenxiaHu (3)
mimakaev (2)
lldelisle (2)
qm713152 (2)
bskubi (2)
golobor (2)
ddepierre (2)
Phlya (2)
ratheraarif (2)
wangfuzhou110 (2)
sfh1111 (2)
ysora (1)
luantune (1)
XunuoZhu (1)

Pull Request Authors

pre-commit-ci[bot] (31)
nvictus (17)
ShigrafS (6)
thomas-reimonn (6)
Phlya (4)
dependabot[bot] (4)
a-detiste (3)
GarrettNg (2)
imSanko (2)
Snowman-cpu (2)
kloetzl (2)
lrauschning (2)
molecule53 (1)
conradbzura (1)
manzt (1)

Top Labels

Issue Labels

enhancement (6) api (2) help wanted (1)

Pull Request Labels

dependencies (4) python (2) github_actions (2)

Packages

Total packages: 1
Total downloads:
- pypi 8,376 last-month
Total docker downloads: 788

Total dependent packages: 22
Total dependent repositories: 64
Total versions: 50
Total maintainers: 2

pypi.org: cooler

Sparse binary format for genomic interaction matrices.

Documentation: https://cooler.readthedocs.io/
License: BSD-3-Clause
Latest release: 0.10.4
published 6 months ago

Versions: 50
Dependent Packages: 22
Dependent Repositories: 64
Downloads: 8,376 Last month
Docker Downloads: 788

Rankings

Dependent packages count: 0.7%

Docker downloads count: 1.2%

Dependent repos count: 1.9%

Average: 2.1%

Downloads: 4.6%

Maintainers (2)

nvictus Open2C

Last synced: 4 months ago

Dependencies

docs/requirements.txt pypi

Sphinx >=1.6
asciitree *
click *
m2r *
mock *
multiprocess *
numpydoc *
pyyaml *
recommonmark *
six *
sphinx-rtd-theme *

requirements-dev.txt pypi

biopython <1.77 development
dask * development
ipytree * development
matplotlib * development
mock * development
psutil * development
pysam * development
pytest * development
pytest-cov * development
pytest-flake8 * development

requirements.txt pypi

asciitree *
click >=7
cytoolz <0.11
h5py >=2.5
multiprocess *
numpy >=1.9
pandas *
pyfaidx *
pypairix *
pyyaml *
scipy >=0.16
simplejson *
six *

.github/workflows/ci.yml actions

actions/checkout v3 composite
actions/setup-python v4 composite
codecov/codecov-action v3 composite

.github/workflows/publish-pypi.yml actions

actions/checkout v3 composite
actions/setup-python v4 composite

cooler

Science Score: 77.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

Cooler

A cool place to store your Hi-C

Installation

Citing

Contributing

Related projects

Affiliations and Acknowledgements

Owner

Citation (CITATION.cff)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

pypi.org: cooler

Rankings

Maintainers (2)

Dependencies