GNN-based single-cell gene expression analysis
Using single-cell gene expression analysis frameworks, like ScanPy, we can go from single-cell "raw" data in .h5ad
format to inferring the cells and genes associated with sample/cell metadata, using ML for scientific discovery.
-
To run these analyses, install
pytorch
andpytorch_geometric
by following these help pages for torch and pyg installation, respectively. -
Install
ScanPy
You can conda
environments and the scnd.yml
file in this repo to install all dependencies