Single-Cell Exploratory Compositional Data Analysis

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Documentation for package ‘scECODA’ version 0.99.9

• DESCRIPTION file
• User guides, package vignettes and other documentation
• Package NEWS
• Package README

Help Pages

calculate_pseudobulk	Calculate Pseudobulk from Count Matrix
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
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