معرفی شرکت ها
cooler-0.9.1
تبلیغات ما
مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشتر
تبلیغات ما
مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشتر
تبلیغات ما
مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشتر
تبلیغات ما
مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشتر
تبلیغات ما
مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشترتوضیحات
Sparse binary format for genomic interaction matrices.
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | cooler-0.9.1 |
| نام | cooler |
| نسخه کتابخانه | 0.9.1 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | ['Open2C <open.chromosome.collective@gmail.com>'] |
| نویسنده | - |
| ایمیل نویسنده | Nezar Abdennur <nabdennur@gmail.com> |
| آدرس صفحه اصلی | - |
| آدرس اینترنتی | https://pypi.org/project/cooler/ |
| مجوز | BSD-3-Clause |
# Cooler
<a href="https://open2c.github.io/cooler"><img width="25%" src="https://github.com/open2c/cooler/raw/master/docs/cooler_logo.png" alt="Cooler"></a>
<table>
<tr>
<td>Latest Release</td>
<td>
<a href="https://pypi.org/project/cooler/">
<img src="https://img.shields.io/pypi/v/cooler?color=blue&label=PyPI%20package" alt="latest release pypi">
</a>
<a href="https://bioconda.github.io/recipes/cooler/README.html">
<img src="https://img.shields.io/conda/vn/bioconda/cooler?color=blue" alt="latest release bioconda">
</a>
</td>
</tr>
<tr>
<td>License</td>
<td>
<a href="https://github.com/open2c/cooler/blob/master/LICENSE">
<img src="https://img.shields.io/badge/license-BSD-green" alt="license">
<!-- <img src="https://img.shields.io/pypi/l/cooler.svg" alt="license"> -->
</a>
</td>
</tr>
<tr>
<td>Build Status</td>
<td>
<a href="https://github.com/open2c/cooler/blob/master/.github/workflows/ci.yml">
<img src="https://github.com/open2c/cooler/actions/workflows/ci.yml/badge.svg" alt="build status">
</a>
</td>
</tr>
<tr>
<td>Pre-commit Status</td>
<td>
<a href="https://results.pre-commit.ci/repo/github/49553222">
<img src="https://results.pre-commit.ci/badge/github/open2c/cooler/master.svg" alt="pre-commit status" />
</a>
</td>
</tr>
<tr>
<td>Docs Status</td>
<td>
<a href="http://cooler.readthedocs.org/en/latest/">
<img src="https://readthedocs.org/projects/cooler/badge/?version=latest">
</a>
</td>
</tr>
<tr>
<td>Coverage</td>
<td>
<a href="https://codecov.io/gh/open2c/cooler">
<img src="https://codecov.io/gh/open2c/cooler/branch/master/graph/badge.svg" alt="coverage">
</a>
</td>
</tr>
<tr>
<td>Downloads</td>
<td>
<a href="https://pypi.org/project/cooler">
<img src="https://static.pepy.tech/personalized-badge/cooler?period=total&units=international_system&left_color=grey&right_color=blue&left_text=PyPI%20downloads" alt="pypi downloads">
</a>
<a href="http://bioconda.github.io/recipes/cooler/README.html">
<img src="https://img.shields.io/conda/dn/bioconda/cooler.svg?style=flat&label=Bioconda downloads" alt="bioconda downloads">
</a>
</td>
</tr>
<tr>
<td>Citation</td>
<td>
<a href="https://doi.org/10.1093/bioinformatics/btz540">
<img src="https://img.shields.io/badge/DOI-10.1093%2Fbioinformatics%2Fbtz540-blue" alt="paper doi">
</a>
<a href="https://zenodo.org/badge/latestdoi/49553222">
<img src="https://zenodo.org/badge/49553222.svg" alt="zenodo doi">
</a>
</td>
</tr>
<tr>
<td>Community</td>
<td>
<a href="https://bit.ly/open2c-slack">
<img src="https://img.shields.io/badge/chat-slack-%233F0F3F?logo=slack" alt="slack">
</a>
</td>
</tr>
</table>
## A cool place to store your Hi-C
Cooler is a support library for a **sparse, compressed, binary** persistent storage [format](http://cooler.readthedocs.io/en/latest/schema.html), 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](https://en.wikipedia.org/wiki/Hierarchical_Data_Format) as the container format. The `cooler` package includes a suite of [command line tools](http://cooler.readthedocs.io/en/latest/cli.html) and a [Python API](http://cooler.readthedocs.io/en/latest/api.html) to facilitate creating, querying and manipulating cooler files.
To get started:
- [Install](#Installation) cooler
- Read the [documentation](http://cooler.readthedocs.org/en/stable/) and see the Jupyter Notebook [walkthrough](https://github.com/open2c/cooler-binder).
- _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](https://data.4dnucleome.org/visualization/index).
### Installation
Install from PyPI using pip.
```sh
$ pip install cooler
```
If you are using `conda`, you can alternatively install `cooler` from the [bioconda](https://bioconda.github.io/index.html) 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](https://doi.org/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](https://github.com/open2c/cooler/blob/master/CONTRIBUTING.md).
### Related projects
- Process Hi-C data with [distiller](https://github.com/open2c/distiller)!
- Downstream analysis with [cooltools](https://github.com/open2c/cooltools)!
- Visualize your cooler data with [HiGlass](http://higlass.io)!
نیازمندی
| مقدار | نام |
|---|---|
| >=1.9 | numpy |
| >=0.16 | scipy |
| >1.0 | pandas |
| >=2.5 | h5py |
| >=7 | click |
| - | cytoolz |
| - | multiprocess |
| - | pyfaidx |
| - | asciitree |
| - | pyyaml |
| - | simplejson |
| - | biopython |
| - | dask[array,dataframe] |
| >=0.2.2 | ipytree |
| >=8.0.0 | ipywidgets |
| - | matplotlib |
| - | pypairix |
| - | psutil |
| - | pysam |
| >=1.6 | Sphinx |
| - | sphinx-rtd-theme |
| - | m2r |
| - | numpydoc |
| - | recommonmark |
| - | coverage[toml] |
| - | flake8 |
| - | flake8-pyproject |
| - | isort |
| - | pytest |
| - | pytest-cov |
زبان مورد نیاز
| مقدار | نام |
|---|---|
| >=3.6 | Python |
نحوه نصب
نصب پکیج whl cooler-0.9.1:
pip install cooler-0.9.1.whl
نصب پکیج tar.gz cooler-0.9.1:
pip install cooler-0.9.1.tar.gz