AddAdj                  Calculate the adjacency matrix given a spatial
                        coordinate matrix
AddParSettingFAST       Add FAST model settings for a PRECASTObj object
CosMx_subset            A Seurat object including spatial
                        transcriptomics dataset from CosMx platform
FAST                    Run FAST model for a PRECASTObj object
FAST_run                (Varitional) ICM-EM algorithm for implementing
                        FAST model
FAST_single             Fit FAST model for single-section SRT data
FAST_structure          (Varitional) ICM-EM algorithm for implementing
                        FAST model with structurized parameters
IntegrateSRTData        Integrate multiple SRT data into a Seurat
                        object
NCFM                    Cell-feature coembedding for scRNA-seq data
NCFM_fast               Cell-feature coembedding for SRT data
RunHarmonyLouvain       Embedding alignment and clustering based on the
                        embeddings from FAST
RuniSCMEB               Fit an iSC-MEB model using the embeddings from
                        FAST
SelectHKgenes           Select housekeeping genes
coembed_plot            Coembedding dimensional reduction plot
coembedding_umap        Calculate UMAP projections for coembedding of
                        cells and features
diagnostic.cor.eigs     Determine the dimension of low dimensional
                        embedding
find.signature.genes    Find the signature genes for each group of
                        cell/spots
get.top.signature.dat   Obtain the top signature genes and related
                        information
get_r2_mcfadden         Calcuate the the adjusted McFadden's pseudo
                        R-square
iscmeb_run              Fit an iSC-MEB model using specified
                        multi-section embeddings
model_set_FAST          Set parameters for FAST model
pbmc3k_subset           A Seurat object including scRNA-seq PBMC
                        dataset
pdistance               Calculate the cell-feature distance matrix
top5_signatures         A data.frame object including top five
                        signature genes in scRNA-seq PBMC dataset
transferGeneNames       Transfer gene names from one fortmat to the
                        other format
