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: ATAC-seq/DNase-seq footprinting method
- THOR: ChIP-Seq differential peak caller
- Motif Analysis: TBFS match and enrichment
- RGT-Viz: Visualization tool
- TDF: DNA/RNA triplex domain finder
See https://reg-gen.readthedocs.io for documentation and tutorials.
We recommend using conda to manage the python environment to avoid issues.
You can install conda from here
Once you successfully installed conda, first create a specific environment:
conda create -n rgt python=3.9Then activate your environment and install the full RGT suite with all other dependencies:
conda activate rgt
pip install RGTDetailed installation instructions and basic problem solving can be found on our website.
Please also consider citing our main paper if you used any sub-tools from RGT:
@article{li2023rgt,
title={RGT: a toolbox for the integrative analysis of high throughput regulatory genomics data},
author={Li, Zhijian and Kuo, Chao-Chung and Ticconi, Fabio and Shaigan, Mina and Gehrmann, Julia and Gusmao, Eduardo Gade and Allhoff, Manuel and Manolov, Martin and Zenke, Martin and Costa, Ivan G},
journal={BMC bioinformatics},
volume={24},
number={1},
pages={1--12},
year={2023},
publisher={BioMed Central}
}