AE | Feature auto encoder class |
calculate_knn_graph | Isolation forest based KNN graph |
GCNModelAE | GCN Model Auto-enccoder |
GCNModelVAE | GCN Model Variational Auto-enccoder auto-encoding variational... |
gene_counts | scRNA-seq gene expression counts from GSE138852 |
gene_counts_small | A subset of GSE138852 scRNA-seq gene expression counts |
generateNetwork | Infer a cell-cell network from the encoded space using... |
GraphCovolution | Graph Convolutional Neural Network Layer |
InnerProductDecoder | Inner Product Decoder |
loss_function_gcn | GCN Loss function |
loss_function_graph | Loss function regularised by the graph information |
plotCellNet | Cell network plotting function |
plotDegree | Show Degree Distribution in Network |
plotLog | Log-log plot of Network |
preprocessCSV | Pre-process scRNA-seq Count Matrix in CSV File |
regulation_mse_loss_function | Regulation MSE Loss Function |
runFeatureAE | Main function of running scGNN feature auto-encoder |
runLTMG | Get discretised regulatory signals from LTMG model |
runscRGNet | Launch Shiny webtool |
scDataset | scRNA-seq dataset class |
setHardware | A hardware setter to run the model |
setHyperParams | Hyper-parameter setter |
train | Main Training Model |
vallina_mse_loss_function | Vallina MSE |
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