eugene-tools 0.1.0

Elucidating the Utility of Genomic Elements with Neural Nets

Elucidating the Utility of Genomic Elements with Neural Nets

EUGENe represents a computational framework for machine learning based modeling of regulatory sequences. It is designed after the Scanpy package for single cell analysis in Python and is meant to make the development of deep learning workflows in the genomics field more findable, accessible, interoperitable and reproducible (FAIR). EUGENe consists of several modules for handling data and for building, training, evaluating and interpreting deep learners that predict annotations of biological sequences. EUGENe is primarily designed to be used through its Python API and we feel that users will get the most out of it by using a notebook interface (i.e. Jupyter).

EUGENe is a package that is still under construction, so there's a chance you'll run into an error or two in the current release. However, catching these errors is incredbily valuable for us! If you run into such errors, have enhancement suggestions, or have any questions, please open an issue! You can read the current documentation here for getting started.

If you use EUGENe for your research, please cite our preprint: Klie et al. bioRxiv 2022