Deep learning analysis of macrophages in response to IL-4

This repository includes codes and data for the analysis of the genetic variation effects on macrophages in response to IL-4 using deep learning. The training datasets were based on the sequencing data at GEO:GSE159630. If you use our findings, codes, or data, please cite:

Hoeksema, et al. Mechanisms underlying divergent responses of genetically distinct macrophages to IL-4. Science Advances, 2021.

Deep neural networks

Software dependencies:

• Python 3
• Keras 2.3.1
• tensorflow 2.1.0
• scikit-learn 0.21.3
• deeplift 0.6.10.0
• biopython 1.76

Training neural networks

The codes and data for training and evaluating neural networks are stored in folder: model_training

The configuration files of well-trained models used in the paper are available on Google Drive.

Scoring nucleotide importance

The codes for interpreting trained models and assigning single-nucleotide importance scores are stored in folder: model_interpretation