recipe cooler

Sparse binary format for genomic interaction matrices

Homepage

https://github.com/mirnylab/cooler

License

BSD / BSD-3-Clause

Recipe

/cooler/meta.yaml

Links

doi: 0.1093/bioinformatics/btz540

package cooler

Versions

0.8.11-0,  0.8.10-0,  0.8.9-0,  0.8.8-0,  0.8.7-0,  0.8.6-0,  0.8.5-0,  0.8.3-0,  0.8.2-1, 

0.8.11-0,  0.8.10-0,  0.8.9-0,  0.8.8-0,  0.8.7-0,  0.8.6-0,  0.8.5-0,  0.8.3-0,  0.8.2-1,  0.8.2-0,  0.8.1-0,  0.7.11-0,  0.7.10-1,  0.7.10-0,  0.7.9-0,  0.7.8-0,  0.7.7-0,  0.7.6-4,  0.7.6-3,  0.7.6-2,  0.7.6-1,  0.7.6-0,  0.7.4-0,  0.7.0-0

Depends

• asciitree

• biopython <1.77

• click >7

• cytoolz

• dask

• h5py >=2.5

• hdf5

• multiprocess

• numpy >=1.9

• pairix

• pandas

• pyfaidx

• pysam >0.8

• python

• pyyaml

• scipy

• simplejson

• six

Required By

• schicexplorer

• cooltools

• basenji

• hint

• pore-c

• coolbox

• hicmatrix

• chromosight

• hic2cool

• fanc

• hicexplorer

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install cooler

and update with:

conda update cooler

or use the docker container:

docker pull quay.io/biocontainers/cooler:<tag>

(see cooler/tags for valid values for <tag>)

Link to this page

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/cooler/README.html)