keras_dna: a wrapper for fast implementation of deep learning models in genomics.

Abstract

Prediction of genomic annotations from DNA sequences using deep learning is today becoming a flourishing field with many applications. Nevertheless, there are still difficulties in handling data in order to conveniently build and train models dedicated for specific end-user's tasks. keras_dna is designed for an easy implementation of Keras models (TensorFlow high level API) for genomics. It can handle standard bioinformatic files formats as inputs such as bigwig, gff, bed, wig, bedGraph or fasta and returns standardized inputs for model training. keras_dna is designed to implement existing models but also to facilitate the development of news models that can have single or multiple targets or inputs. Freely available with a MIT License using pip install keras_dna or cloning the github repo at https://github.com/etirouthier/keras_dna.git. Supplementary data are available at Bioinformatics online.