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zes017 committed Jul 20, 2020
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[![python-version](https://img.shields.io/badge/python-3.6+-blue.svg)](https://www.python.org/downloads/release/python-360/)
[![contributions welcome](https://img.shields.io/badge/contributions-welcome-brightgreen.svg?style=flat)](https://github.com/zeyang-shen/maggie/issues)
[![DOI](https://zenodo.org/badge/DOI/10.1101/2020.01.30.925917.svg)](https://doi.org/10.1093/bioinformatics/btaa476)
[![DOI](https://zenodo.org/badge/DOI/10.1093/bioinformatics/btaa476.svg)](https://doi.org/10.1093/bioinformatics/btaa476)

# MAGGIE
MAGGIE provides a framework for identifying DNA sequence motifs mediating transcription factor binding and function. By leveraging measurements and genetic variation information from different genotypes (human individuals, animal strains, or alleles), MAGGIE associates the mutation of DNA sequence motif with various types of epigenomic features, including but not limited to transcription factor binding, open chromatin, histone modification, and stimulus response of regulatory elements.
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Please go to our [wiki page](https://github.com/zeyang-shen/maggie/wiki) for more detailed usage of MAGGIE.

## Citation
If you use the algorithms described in MAGGIE, the software, or the NK-$\kappa$b ChIP-seq data at [GEO:GSE144070](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE144070), please cite
If you use our findings, the software, or the NF-kb ChIP-seq data at [GEO:GSE144070](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE144070), please cite

[Shen, et al. MAGGIE: leveraging genetic variation to identify DNA sequence motifs mediating transcription factor binding and function. Bioinformatics, 2020](https://doi.org/10.1093/bioinformatics/btaa476)

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