Training and using TFFM/PSSM/4-bits + DNA shape classifiers
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README.md

DNAshapedTFBS

Python module for TFFM/PSSM/4-bits + DNA shape classifiers

This module allows for:

  1. Training PSSM/TFFM/4-bits + DNA shape classifiers on ChIP-seq data
  2. Applying PSSM/TFFM/4-bits + DNA shape classifiers on ChIP-seq data

Note that only the best hit per ChIP-sequence is considered in the current version of the module.

Dependencies

The module requires:

Tutorial

You can find some examples of how to run the DNAshapedTFBS.py tool in the script test.sh provided in the test/ repository of this package.

The script feature_importance_heatmap.py plots the heatmap(s) of trained classifier(s). Note that the current version only works for PSSM/TFFM + DNA shape classifiers. You can get help on how to use it by typing

python2.7 feature_importance_heatmap.py -h

Project home page

For information on the source tree, examples, issues, and pull requests, see

http://github.com/amathelier/DNAshapedTFBS

Cite

If you use the DNAshapedTFBS tool, please cite

  • A. Mathelier, B. Xin, T.-P. Chiu, L. Yang, R.R. Rohs, and W.W. Wasserman (2016) DNA shape features improve transcription factor binding site predictions in vivo. Cell Systems, DOI:10.1016/j.cels.2016.07.001.