| .RunLTMG | Run Left-truncated mixed Gaussian | 
| ATAC_net | Results of ConNetGNN() for scATAC-seq data from SNARE-seq dataset | 
| BIC_LTMG | BIC_LTMG | 
| BIC_ZIMG | BIC_ZIMG | 
| ConNetGNN | Construct association networks for gene-gene, cell-cell, and gene-cell based on graph neural network (GNN) | 
| ConNetGNN_data | The results of ConNetGNN() function | 
| cpGModule | Identify cell phenotype activated gene module | 
| create_scapGNN_env | Create the create_scapGNN_env environment on miniconda | 
| Fit_LTMG | Fitting function for Left-truncated mixed Gaussian | 
| Global_Zcut | Global_Zcut | 
| H9_0h_cpGM_data | Cell-activated gene modules under the 0-hour phenotype | 
| H9_24h_cpGM_data | Cell-activated gene modules under the 24-hour phenotype | 
| H9_36h_cpGM_data | Cell-activated gene modules under the 36-hour phenotype | 
| Hv_exp | Single-cell gene expression profiles | 
| instPyModule | Install the pyhton module through the reticulate R package | 
| InteNet | Integrate network data from single-cell RNA-seq and ATAC-seq | 
| isLoaded | The internal functions of the 'scapGNN' package | 
| load_path_data | load pathway or gene set's gmt file | 
| LTMG | Left-truncated mixed Gaussian | 
| LTMG-class | An S4 class to represent the input data for LTMG. | 
| plotCCNetwork | Visualize cell cluster association network graph | 
| plotGANetwork | Visualize gene association network graph of a gene module or pathway at the specified cell phenotype | 
| plotMulPhenGM | Visualize gene association network graph for activated gene modules under multiple cell phenotypes | 
| Preprocessing | Data preprocessing | 
| Pure_CDF | Pure_CDF | 
| RNA_ATAC_IntNet | Results of InteNet() for integrating scRNA-seq and scATAC-seq data. | 
| RNA_net | Results of ConNetGNN() for scRNA-seq data from SNARE-seq dataset | 
| RunLTMG | Run Left-truncated mixed Gaussian | 
| RunLTMG-method | Run Left-truncated mixed Gaussian | 
| RWR | Function that performs a random Walk with restart (RWR) on a given graph | 
| scPathway | Infer pathway activation score matrix at single-cell resolution | 
| scPathway_data | Single cell pathway activity matrix |