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Toolkit to perform regulatory genomics data analysis

Project description

RGT - Regulatory Genomics Toolbox

Latest version released on PyPi Build status of the develop branch Test coverage

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.

Project details


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Files for RGT, version 0.13.1
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