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.
TF-COMB can be quickly installed via pip:
$ pip install TF-COMBOr 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 .
Please visit the full documentation at: tf-comb.readthedocs.io
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