GRN_params_100          100_gene_GRN is a matrix of GRN params
                        consisting of 100 genes where: # - column 1 is
                        the target gene ID, # - column 2 is the gene ID
                        which acts as a transcription factor for the
                        target (regulated) gene # - column 3 is the
                        effect of the column 2 gene ID on the column 1
                        gene ID
GRN_params_1139         GRN_params_1139 is a matrix of GRN params
                        consisting of 1139 genes where: # - column 1 is
                        the target gene ID, # - column 2 is the gene ID
                        which acts as a transcription factor for the
                        target (regulated) gene # - column 3 is the
                        effect of the column 2 gene ID on the column 1
                        gene ID
Get_1region_ATAC_correlation
                        This function gets the average correlation rna
                        seq counts and region effect on genes for genes
                        which are only associated with 1 chromatin
                        region
Get_ATAC_correlation    This function gets the average correlation rna
                        seq counts and chromatin region effect on genes
Phyla1                  Creating a linear example tree
Phyla3                  Creating an example tree with 3 tips
Phyla5                  Creating an example tree with 5 tips
True2ObservedATAC       Simulate observed ATAC-seq matrix given
                        technical noise and the true counts
True2ObservedCounts     Simulate observed count matrix given technical
                        biases and the true counts
add_expr_noise          Add experimental noise to true counts
add_outliers            Add outliers to the observed counts
cci_cell_type_params    Generate cell-type level CCI parameters
dens_nonzero            this is the density function of log(x+1), where
                        x is the non-zero values for ATAC-SEQ data
divide_batches          Divide batches for observed counts
gen_clutter             generate a clutter of cells by growing from the
                        center
gene_corr_cci           Plot the ligand-receptor correlation summary
gene_corr_regulator     Print the correlations between targets of each
                        regulator
plot_cell_loc           Plot cell locations
plot_gene_module_cor_heatmap
                        Plot the gene module correlation heatmap
plot_grid               Plot the CCI grid
plot_grn                Plot the GRN network
plot_phyla              Plot a R phylogenic tree
plot_rna_velocity       Plot RNA velocity as arrows on tSNE plot
plot_tsne               Plot t-SNE visualization of a data matrix
run_shiny               Launch the Shiny App to configure the
                        simulation
scmultisim_help         Show detailed documentations of scMultiSim's
                        parameters
sim_example             Simulate a small example dataset with 200 cells
                        and the 100-gene GRN
sim_example_spatial     Simulate a small example dataset with 200 cells
                        and the 100-gene GRN, with CCI enabled
sim_true_counts         Simulate true scRNA and scATAC counts from the
                        parameters
spatialGrid-class       The class for spatial grids
