calc_anosim             Analysis of Similarities (ANOSIM) R score
calc_ari                Calculate Adjusted Rand Index (ARI)
calc_clr                Perform the Centered Log-Ratio (CLR)
                        transformation.
calc_freq               Calculate relative frequencies (percentages)
                        column-wise.
calc_modularity         Calculate Adjusted Modularity Score
calc_sil                Calculate Average Silhouette Width
calculate_pseudobulk    Calculate Pseudobulk from Count Matrix
compute_KNN_from_dist   Compute K-Nearest Neighbors (KNN) from Distance
                        Matrix
compute_snn_graph       Compute Shared Nearest Neighbor (SNN) Graph
create_long_data        Reshapes ECODA data into a long format for
                        plotting and analysis.
deseq2_normalize        DESeq2 Normalization of Pseudobulk Data
ecoda                   Create an SummarizedExperiment object from
                        various data types
ecoda_helper            Core constructor for SummarizedExperiment
                        objects from count/frequency matrices
example_data            Example Data for scECODA
find_hvcs               Identifies and stores Highly Variable Cell
                        Types (HVCs) in an SummarizedExperiment object.
get_celltype_counts     Get the cell type counts from a long data frame
                        (e.g. seurat object metadata) where each cell
                        is a row.
get_celltype_variances
                        Calculates the variance of cell types across
                        samples.
get_ecoda_assay         Helper to get assay for ecoda
                        SummarizedExperiment objects
get_hvcs                Selects Highly Variable Cell Types (HVCs) based
                        on variance or count threshold.
get_sample_metadata     Extracts constant metadata for each sample from
                        a cell-level data frame.
plot_barplot            Generates a Stacked Bar Plot of Cell Type
                        Relative Abundance.
plot_boxplot            Generates Boxplots for CLR-transformed Cell
                        Type Abundances with Optional Group Comparison.
plot_corr               Plot Cell Type Correlation Matrix
plot_heatmap            Generates a Heatmap of Cell Abundance Data from
                        an SummarizedExperiment assay.
plot_pca                Plot Principal Component Analysis and Calculate
                        Clustering Scores
plot_pca3d              Plot 3-dimensional interactive Principal
                        Component Analysis plot
plot_varmean            Generates a Mean-Variance Plot for
                        CLR-transformed Cell Type Data.
replace_zeros           Replace zero values in count or frequency data
