SNEEP: SNV exploration and functional analysis using epigenetic data
SNEEP is a fast method to identify regulatory Single Nucleotid Variations (rSNVs) that modify the binding sites of Transcription Factors (TFs) for large collections of SNPs or SNVs provided by the user.
Documentation
The full documentation is available on Read the Docs
News
- 06.05.2024. Our paper that explains the statistical approach of SNEEP got published in iScience
- 26.7.2023. Our paper about a first application with SNEEP got published in Human Genomics
Versions
- April 22th, 2024: v1.1: fixed an issue with the epsilon parameter
- March 18th 2024: v1.0: We are happy to upload the offical first version of our software
References
For our statistical approach, please cite:
Nina Baumgarten, Laura Rumpf, Thorsten Kessler, Marcel H. Schulz (2024), A statistical approach for identifying single nucleotide variants that affect transcription factor binding, iScience, pdf, web
We used our statistical approach to determine non-coding disease genes in cardiovascular diseasee. For more details see:
Chaonan Zhu, Nina Baumgarten, Meiqian Wu, Yue Wang, Arka Provo Das, Jaskiran Kaur, Fatemeh Behjati Ardakani, Thanh Thuy Duong, Minh Duc Pham, Maria Duda, Stefanie Dimmeler, Ting Yuan, Marcel H. Schulz, Jaya Krishnan (2023), CVD-associated SNPs with with regulatory potential reveal novel non-coding disease genes, Human Genomics 2023 full text