TIMON

Transcription Factor Interaction Inference from Motif Co-occurrence Networks (TIMON) is a tool to analyze transcription factor (TF) motif co-occurrences from epigenetic datasets (open chromatin, transcription factor binding sites, enhancers, etc.). The first step of TIMON is to identify non-overlapping motifs to identify the best matching TFs in the sequences of interest. Next, TIMON builds co-occurrences matrices between TFs. Through comparing the TF co-occurrences in the cell type of interest with background cell types (50+ cell types from ENCODE), TIMON identifies significantly enriched TF pair in the cell type of interest and thus construct the TF co-occurrence networks.

For questions on installation or usage, please open an issue, submit a pull request, or contact Rick Z. Li (zhl022@ucsd.edu)

Installation

git clone https://github.com/rzzli/TIMON.git
cd TIMON
pip install -e .

optional: install in a new conda environment

conda create -n timon_conda python=3.7.7
conda activate timon_conda
git clone https://github.com/rzzli/TIMON.git
cd TIMON
pip install -e .

add the new conda environment to jupyter

conda activate timon_conda
python -m ipykernel install --user --name timon_conda

The tutorial requires PyGraphviz package, to install:

conda install --channel conda-forge pygraphviz

Uninstall TIMON/conda environment

uninstall TIMON package

pip uninstall TIMON

remove the conda environment

conda env remove -n timon_conda

remove the conda environment on jupyter notebook

jupyter kernelspec uninstall timon_conda

import TIMON

from TIMON.motifFreq import *

Tutorials

This section is actively under development.

• Fetal and Postnatal microglia motif co-occurrence analysis.

License

This project is licensed under MIT

Contribution

TIMON was developed primarily by Rick Z Li, with contributions and suggestions from Claudia Han and supervision from Christopher Glass.