https://github.com/thomasmbury/fatenet

https://github.com/thomasmbury/fatenet

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• Host: GitHub
• URL: https://github.com/thomasmbury/fatenet
• Owner: ThomasMBury
• Created: 2024-06-16T17:09:22.000Z (7 months ago)
• Default Branch: main
• Last Pushed: 2024-09-04T15:01:21.000Z (4 months ago)
• Last Synced: 2024-10-12T15:51:05.697Z (3 months ago)
• Language: HTML
• Size: 23 MB
• Stars: 1
• Watchers: 1
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# FateNet

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

## Directories

- ```/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

## Data availability

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```.