novapyth / reg-gen

Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.

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:

• 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

Installation

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.