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: 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.

Installation with conda

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=3.9

Then activate your environment and install the full RGT suite with all other dependencies:

conda activate rgt
pip install RGT

Detailed 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}
}