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
auc_bar                 Bar plot of AUCs from validating data sets
auc_stat                Extract AUC statistics in coclustering
                        optimization
auc_violin              Plot extracted AUCs by parameter settings
cluster_cell            Cluster single cells or combination of single
                        cells and bulk
coclus_opt              Optimizing coclustering process with two levels
                        of parallelizations available.
coclus_roc              Co-cluster bulk and single cell data Calculate
                        ROC/AUC for the combined bulk and single cell
                        data
cocluster               Coclustering bulk and single cell data in a
                        single run
com_factor              Combine Factors in Targets File
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
desired_bulk_shiny      Integrated Shiny App
edit_tar                Edit Targets Files
filter_cell             Filter single cell data separately in a list
filter_data             Filter the Data Matrix
filter_iter             Iteratively filter bulk and single data
                        according to parameters in a data frame.
lis.deg.up.down         A nested list of differentialy-expressed genes
                        (DEGs) detected by different methods
matrix_hm               Matrix Heatmap
mean_auc_bar            Plot mean of extracted AUCs by parameter
                        settings
network                 Visualize a Target Assayed Item in a Network
                        Graph
norm_data               Normalize Sequencing Count Matrix
norm_multi              Normalize one or multiple count data sets.
plot_dim                Plotting single cells in reduced
                        dimensionalities
profile_gene            Plot Gene Expression Profiles in a Data Frame
random_para             Generate random combinations of parameter
                        settings
read_cache              Read R Objects from Cache
read_fr                 Import Data from Tabular Files
read_hdf5               Read Data from the Shiny App Database
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
spd_auc_violin          Violin plot of extracted AUCs by top spd.sets
sub_asg                 Subset the bulk-cell assignments
sub_data                Subset Target Data for Spatial Enrichment
submatrix               Subset Target Assayed Items and Their Nearest
                        Neighbors
true_bulk               Assign true bulk to cells in 'colData' slot.
update_feature          Update aSVG Spatial Features
write_hdf5              Construct Database for the Shiny App
