| adj_mod | Computing adjacency matrix and identifying network modules |
| aggr_rep | Aggregate "Sample__Condition" Replicates in Data Matrix |
| aSVG.remote.repo | A list of URLs of remote aSVG repos |
| cell_group | Add manual cell group labels to SingleCellExperiment |
| 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... |
| custom_shiny | Create Customized spatialHeatmap Shiny Apps |
| cut_dendro | Cutting dendrograms |
| cvt_id | Converting gene ids using annotation databases |
| database | Creat databases for the Shiny App |
| data_ref | Calculating relative expression values |
| edit_tar | Edit Targets Files |
| filter_data | Filtering the Data Matrix |
| matrix_hm | Hierarchical clustering combined with matrix heatmap |
| network | Network graphs |
| norm_cell | Normalizing single cell data |
| norm_data | Normalize Sequencing Count Matrix |
| norm_srsc | Jointl normalization of spatially resolved single cell data... |
| opt_bar | Bar plots of co-clustering optimization results. |
| optimal_k | Using the elbow method to find the optimal number of clusters... |
| 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... |
| plot_kmeans | Plotting the clusters returned by K-means clustering |
| plot_meta | Meta function for plotting spatial heatmaps or co-visualizing... |
| 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_svg | Parsing annotated SVG (aSVG) files |
| reduce_dim | Reducing dimensionality in count data |
| reduce_rep | Reduce sample replicates |
| return_feature | Return aSVG Files Relevant to Target Features |
| save_cache | Save R Objects in Cache |
| shiny_shm | Integrated Shiny App |
| shm | Plot Spatial Heatmaps |
| SpatialEnrichment | Identifying spatially enriched or depleted biomolecules |
| spatialHeatmap-package | spatialHeatmap Spatial Heatmap, Spatial Enrichment, Data... |
| spatial_hm | Plot Spatial Heatmaps |
| SPHM | The SPHM class |
| SPHMMethods | Methods for S4 class 'SPHM' |
| submatrix | Subsetting data matrix |
| SVG | The SVG class for storing annotated SVG (aSVG) instances |
| SVGMethods | Methods for S4 class 'SVG' |
| true_bulk | Assign true bulk to cells in 'colData' slot. |
| update_feature | Update aSVG Spatial Features |
| write_svg | Exporting each spatial heatmap to a separate SVG file |
