General purpose stuff to generate and process Hi-C data in its simplest form

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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

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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

Project details

Verified details

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