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
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
InteNet                 Integrate network data from single-cell RNA-seq
                        and ATAC-seq
LTMG                    Left-truncated mixed Gaussian
LTMG-class              An S4 class to represent the input data for
                        LTMG.
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
RWR                     Function that performs a random Walk with
                        restart (RWR) on a given graph
RunLTMG                 Run Left-truncated mixed Gaussian
cpGModule               Identify cell phenotype activated gene module
create_scapGNN_env      Create the create_scapGNN_env environment on
                        miniconda
instPyModule            Install the pyhton module through the
                        reticulate R package
isLoaded                The internal functions of the 'scapGNN' package
load_path_data          load pathway or gene set's gmt file
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
scPathway               Infer pathway activation score matrix at
                        single-cell resolution
scPathway_data          Single cell pathway activity matrix
