TF-COMB

TF-COMB stands for “Transcription Factor Co-Occurrence using Market Basket analysis” and is a python module for identifying co-occurring TFs in regulatory regions.

With a flexible input of ChIP-seq peaks, motif positions, footprint locations, ATAC-seq peaks etc., TF-COMB utilizes a modified market basket analysis to identify TFs (or regions) which are highly co-occurring. The identified TF pairs can then be analyzed in more detail using downstream analysis such as:

• Preferred distance between TFs
• Orientation of stranded regions
• Differential co-occurrence between conditions
• Network analysis to identify protein hubs

Please visit the Examples to see modes of usage.

Installation

TF-COMB can be quickly installed via pip:

$ pip install TF-COMB

Or directly from the github repository using the required_packages in a conda (mamba) environment:

$ mamba create -n tfcomb_env --file required_packages.txt
$ conda activate tfcomb_env 
$ pip install .

Usage

Please visit the full documentation at: tf-comb.readthedocs.io

How to cite

Bentsen M, Heger V, Schultheis H, Kuenne C, Looso M. TF-COMB - Discovering grammar of transcription factor binding sites. Comput Struct Biotechnol J. 2022 Jul 21;20:4040-4051

DOI: https://doi.org/10.1016/j.csbj.2022.07.025