This is the repository to accompany the article:
FateNet: an integration of dynamical systems and deep learning for cell fate prediction. Mehrshad Sadria and Thomas M. Bury https://www.biorxiv.org/content/10.1101/2024.01.16.575913v1
/code/training_data: Generate training data for the neural network classifiers/code/dl_train: Train the neural network classifiers/code/simple_gene_model: Evaluate FateNet on simulation of simple gene network/code/sergio: Evaluate FateNet on SERGIO simulation/code/pancreas: Evaluate FateNet on pancreas data/code/weinreb_klein: Evaluate FateNet on hematopoiesis data
The simulated scRNA-seq data from SERGIO can be found at: https://github.com/PayamDiba/SERGIO.
The hematopoiesis data from Weinreb et al. can be downloaded from GEO under accession number GSE140802.
The simulated scRNA-seq data generated by the simple gene regulatory network is saved in /code/simple_gene_model/output.