SVG-class               The SVG class for storing annotated SVG (aSVG)
                        instances
SVGMethods              Methods for S4 class 'SVG'
aSVG.remote.repo        A list of URLs of remote aSVG repos
adj_mod                 Compute Adjacency Matrix and Identify Modules
aggr_rep                Aggregate "Sample__Condition" Replicates in
                        Data Matrix
cluster_cell            Cluster single cells or combination of single
                        cells and bulk
coclus_opt              Optimization of co-clustering bulk and single
                        cell data
cocluster               Co-clustering bulk and single cell data
com_factor              Combine Factors in Targets File
covis                   Co-visualizing spatial heatmaps with single
                        cell embedding plots
custom_shiny            Create Customized Shiny App of Spaital Heatmap
deg.table               A table of differentialy-expressed genes (DEGs)
                        detected by different methods
deg_ovl                 Plot Overlap of Spatially-Enriched Genes Across
                        Methods
edit_tar                Edit Targets Files
filter_data             Filter the Data Matrix
graph_line              Plot Gene Expression Profiles in a Data Frame
lis.deg.up.down         A nested list of differentialy-expressed genes
                        (DEGs) detected by different methods
manual_group            Add manual cell group labels to
                        SingleCellExperiment
matrix_hm               Matrix Heatmap
network                 Visualize a Target Assayed Item in a Network
                        Graph
norm_cell               Normalizing single cell data
norm_data               Normalize Sequencing Count Matrix
opt_bar                 Bar plots of co-clustering optimization
                        results.
opt_setting             Bar plots of co-clustering optimization
                        results.
opt_violin              Violin plots of co-clustering validation
                        results
plot_dim                Embedding plots of single cells/bulk tissues
                        after co-clustering
process_cell_meta       Processing single cell RNA-seq count data
qc_cell                 Quality control in single cell data
read_cache              Read R Objects from Cache
read_fr                 Import Data from Tabular Files
read_hdf5               Read Data from the Shiny App Database
read_svg                Parsing annotated SVG (aSVG) files
reduce_dim              Reducing dimensionality in count data
reduce_rep              Reduce sample replicates
refine_cluster          Refine single cell clusters
return_feature          Return aSVG Files Relevant to Target Features
save_cache              Save R Objects in Cache
shiny_shm               Integrated Shiny App
spatialHeatmap-package
                        spatialHeatmap Spatial Heatmap, Matrix Heatmap,
                        Network
spatial_enrich          Identify Spatial Feature-Specifcally Expressed
                        Genes
spatial_hm              Plot Spatial Heatmaps
submatrix               Subset Target Assayed Items and Their Nearest
                        Neighbors
tar_ref                 Subset Target Data for Spatial Enrichment
true_bulk               Assign true bulk to cells in 'colData' slot.
update_feature          Update aSVG Spatial Features
write_hdf5              Construct Database for the Shiny App
