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All Projects → CostaLab → reg-gen

CostaLab / reg-gen

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

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bioinformaticsdnase-seqgenomicsngschip-seqatac-seqfootprintingdifferential-peak-calling

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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:

pip3 install --user cython numpy scipy

Then install the full RGT suite with all other dependencies:

pip3 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
python3 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.

Note that the project description data, including the texts, logos, images, and/or trademarks, for each open source project belongs to its rightful owner. If you wish to add or remove any projects, please contact us at [email protected].