Skip to main content
Join the official 2019 Python Developers SurveyStart the survey!

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 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

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


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for RGT, version 0.12.3
Filename, size File type Python version Upload date Hashes
Filename, size RGT-0.12.3.tar.gz (41.9 MB) File type Source Python version None Upload date Hashes View hashes

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN SignalFx SignalFx Supporter DigiCert DigiCert EV certificate StatusPage StatusPage Status page