# reg-gen

**Repository Path**: reyear/reg-gen

## Basic Information

- **Project Name**: reg-gen
- **Description**: github 同步过来的
- **Primary Language**: Unknown
- **License**: Not specified
- **Default Branch**: master
- **Homepage**: None
- **GVP Project**: No

## Statistics

- **Stars**: 0
- **Forks**: 0
- **Created**: 2023-01-31
- **Last Updated**: 2023-01-31

## Categories & Tags

**Categories**: Uncategorized

**Tags**: None

## README

[![Stars](https://img.shields.io/github/stars/CostaLab/reg-gen?logo=GitHub&color=yellow)](https://github.com/CostaLab/reg-gen/stargazers)
[![PyPI](https://img.shields.io/pypi/v/rgt?logo=PyPI)](https://pypi.org/project/RGT/)
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[![Docs](https://readthedocs.org/projects/reg-gen/badge/?version=latest)](https://reg-gen.readthedocs.io)

# RGT - Regulatory Genomics Toolbox

RGT is an open source Python 3.6+ library for analysis of regulatory genomics. RGT is programmed in an oriented object fashion and its core classes provide functionality for handling regulatory genomics data.

The toolbox is made of a core library and several tools:

* [HINT](https://reg-gen.readthedocs.io/en/latest/hint/introduction.html): ATAC-seq/DNase-seq footprinting method
* [THOR](https://reg-gen.readthedocs.io/en/latest/thor/introduction.html):
ChIP-Seq differential peak caller
* [Motif Analysis](https://reg-gen.readthedocs.io/en/latest/motif_analysis/introduction.html): TBFS match and enrichment
* [RGT-Viz](https://reg-gen.readthedocs.io/en/latest/rgt-viz/introduction.html): Visualization tool
* [TDF](https://reg-gen.readthedocs.io/en/latest/tdf/introduction.html): DNA/RNA triplex domain finder

See https://reg-gen.readthedocs.io for documentation and tutorials.

# Installation

The quickest and easiest way to get RGT is to to use pip. First some dependencies:

```shell
pip install --user cython numpy scipy
```

Then install the full RGT suite with all other dependencies:
```shell
pip install --user RGT
```

Detailed installation instructions and basic problem solving can be found on our [website](https://reg-gen.readthedocs.io/en/latest/rgt/installation.html).