General purpose stuff to generate and process Hi-C data in its simplest form
Project description
(csv files) as well as instaGRAAL format.
Home-page: https://github.com/baudrly/hicstuff
Author: lyam.baudry@pasteur.fr
License: GPLv3
Description: # hicstuff
[![PyPI version](https://badge.fury.io/py/hicstuff.svg)](https://badge.fury.io/py/hicstuff)
![PyPI - Python Version](https://img.shields.io/pypi/pyversions/hicstuff.svg)
[![Read the docs](https://readthedocs.org/projects/hicstuff/badge)](https://hicstuff.readthedocs.io)
[![License: GPLv3](https://img.shields.io/badge/License-GPL%203-0298c3.svg)](https://opensource.org/licenses/GPL-3.0)
[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/ambv/black)
A lightweight library that generates and handles Hi-C contact maps in either CSV or [instaGRAAL](https://github.com/koszullab/instaGRAAL) format.
## Installation
```sh
pip3 install hicstuff
```
## Usage
### Contact map generation
```sh
yahcp -1 reads_forward.fastq -2 reads_reverse.fastq -f genome.fa [-s size] [-o output_directory] [-e enzyme] [-q quality_min] [--duplicates] [--clean-up]
```
See [yahcp](https://github.com/baudrly/yahcp) for more information.
### Contact map visualization
```sh
vizmap -h
```
### Library
See the documentation on [reathedocs](https://hicstuff.readthedocs.io).
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Visualization
Classifier: Operating System :: Microsoft :: Windows
Classifier: Operating System :: POSIX
Classifier: Operating System :: Unix
Classifier: Operating System :: MacOS
Requires-Python: >=3.4
Description-Content-Type: text/markdown
Home-page: https://github.com/baudrly/hicstuff
Author: lyam.baudry@pasteur.fr
License: GPLv3
Description: # hicstuff
[![PyPI version](https://badge.fury.io/py/hicstuff.svg)](https://badge.fury.io/py/hicstuff)
![PyPI - Python Version](https://img.shields.io/pypi/pyversions/hicstuff.svg)
[![Read the docs](https://readthedocs.org/projects/hicstuff/badge)](https://hicstuff.readthedocs.io)
[![License: GPLv3](https://img.shields.io/badge/License-GPL%203-0298c3.svg)](https://opensource.org/licenses/GPL-3.0)
[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/ambv/black)
A lightweight library that generates and handles Hi-C contact maps in either CSV or [instaGRAAL](https://github.com/koszullab/instaGRAAL) format.
## Installation
```sh
pip3 install hicstuff
```
## Usage
### Contact map generation
```sh
yahcp -1 reads_forward.fastq -2 reads_reverse.fastq -f genome.fa [-s size] [-o output_directory] [-e enzyme] [-q quality_min] [--duplicates] [--clean-up]
```
See [yahcp](https://github.com/baudrly/yahcp) for more information.
### Contact map visualization
```sh
vizmap -h
```
### Library
See the documentation on [reathedocs](https://hicstuff.readthedocs.io).
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Visualization
Classifier: Operating System :: Microsoft :: Windows
Classifier: Operating System :: POSIX
Classifier: Operating System :: Unix
Classifier: Operating System :: MacOS
Requires-Python: >=3.4
Description-Content-Type: text/markdown
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