open2c / Cooler
Licence: bsd-3-clause
A cool place to store your Hi-C
Stars: ✭ 112
Programming Languages
python
139335 projects - #7 most used programming language
Projects that are alternatives of or similar to Cooler
Dram
Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
Stars: ✭ 47 (-58.04%)
Mutual labels: bioinformatics, genomics
Bgt
Flexible genotype query among 30,000+ samples whole-genome
Stars: ✭ 72 (-35.71%)
Mutual labels: bioinformatics, genomics
Dna Nn
Model and predict short DNA sequence features with neural networks
Stars: ✭ 59 (-47.32%)
Mutual labels: bioinformatics, genomics
Cgranges
A C/C++ library for fast interval overlap queries (with a "bedtools coverage" example)
Stars: ✭ 111 (-0.89%)
Mutual labels: bioinformatics, genomics
Awesome 10x Genomics
List of tools and resources related to the 10x Genomics GEMCode/Chromium system
Stars: ✭ 82 (-26.79%)
Mutual labels: bioinformatics, genomics
Sns
Analysis pipelines for sequencing data
Stars: ✭ 43 (-61.61%)
Mutual labels: bioinformatics, genomics
Ariba
Antimicrobial Resistance Identification By Assembly
Stars: ✭ 96 (-14.29%)
Mutual labels: bioinformatics, genomics
Minimap2
A versatile pairwise aligner for genomic and spliced nucleotide sequences
Stars: ✭ 912 (+714.29%)
Mutual labels: bioinformatics, genomics
Svtyper
Bayesian genotyper for structural variants
Stars: ✭ 79 (-29.46%)
Mutual labels: bioinformatics, genomics
Sibeliaz
A fast whole-genome aligner based on de Bruijn graphs
Stars: ✭ 76 (-32.14%)
Mutual labels: bioinformatics, genomics
Genomics
A collection of scripts and notes related to genomics and bioinformatics
Stars: ✭ 101 (-9.82%)
Mutual labels: bioinformatics, genomics
Gatk
Official code repository for GATK versions 4 and up
Stars: ✭ 1,002 (+794.64%)
Mutual labels: bioinformatics, genomics
Smudgeplot
Inference of ploidy and heterozygosity structure using whole genome sequencing data
Stars: ✭ 98 (-12.5%)
Mutual labels: bioinformatics, genomics
Bwa
Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
Stars: ✭ 970 (+766.07%)
Mutual labels: bioinformatics, genomics
Gubbins
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
Stars: ✭ 67 (-40.18%)
Mutual labels: bioinformatics, genomics
Tiledb Vcf
Efficient variant-call data storage and retrieval library using the TileDB storage library.
Stars: ✭ 26 (-76.79%)
Mutual labels: bioinformatics, genomics
Awesome Sequencing Tech Papers
A collection of publications on comparison of high-throughput sequencing technologies.
Stars: ✭ 21 (-81.25%)
Mutual labels: bioinformatics, genomics
Fastq.bio
An interactive web tool for quality control of DNA sequencing data
Stars: ✭ 76 (-32.14%)
Mutual labels: bioinformatics, genomics
Genomicsqlite
Genomics Extension for SQLite
Stars: ✭ 90 (-19.64%)
Mutual labels: bioinformatics, genomics
Cooler
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 at
ftp://cooler.csail.mit.edu/coolers. - Many more multires (mcool) files are available on the 4DN data portal.
Installation
Install from PyPI using pip.
$ pip install cooler
If you are using conda, you can alternatively install cooler from the bioconda channel.
$ 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 thecondapackage manager to install scientific packages like these. To get it, you can either install the full Anaconda Python distribution or just the standalone conda package manager.
See the docs 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.
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.
@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
Note that the project description data, including the texts, logos, images, and/or trademarks,
for each open source project belongs to its rightful owner.
If you wish to add or remove any projects, please contact us at [email protected].