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:
- THOR: ChIP-Seq differential peak caller, replaces ODIN
- Motif Analysis: TBFS match and enrichment
- HINT: DNase-Seq footprinting method
- RGT-Viz: Visualization tool
- TDF: DNA/RNA triplex domain finder
Python 2 is no longer supported.
The quickest and easiest way to get RGT is to to use pip. First some dependencies:
pip install --user cython numpy scipy
Then install the full RGT suite with all other dependencies:
pip install --user RGT
Alternatively (but not recommended), you can clone this repository:
git clone https://github.com/CostaLab/reg-gen.git
or download a specific release, then proceed to manual installation:
cd reg-gen python setup.py install --user
Detailed installation instructions and basic problem solving can be found on our website.
For any issues, please write to our support mailing list.