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Table 2 Table of exported functions and their descriptions available through the animalcules R package

From: animalcules: interactive microbiome analytics and visualization in R

Data and interface
 run_animalcules() Initiates a local instance of the animalcules Shiny application
Data summary and manipulation
 filter_summary_bar_density() Visualize sample/microbe data with a bar plot (categorical) or density plot (continuous)
 filter_summary_pie_box() Visualize sample/microbe data with a pie chart (categorical) or box plot (continuous)
 filter_categorize() Convert continuous variables into a various number of factors
 counts_to_logcpm() Covert counts table to a log counts per million table
 counts_to_relabu() Covert counts table to a relative abundances table
 upsample_counts() Up-sample counts table to a higher taxon level
 find_taxonomy() Find taxonomy for unlimited ids
 find_taxon_mat() Find taxonomy information matrix for unlimited ids
 mae_pick_samples() Isolate or discard samples from a multi-assay experiment object
 mae_pick_organisms() Isolate or discard microbes from a multi-assay experiment object
Sample level visualization
 relabu_barplot() Generate stacked bar plots of sample and group level microbe relative abundances
 relabu_boxplot() Generate box plots comparing organism prevalence across groups of samples
 relabu_heatmap() Generate a sample by microbe heatmap of counts
 dimred_pca() Return a 2D/3D scatter plot for dimensionality reduction through PCA
 dimred_pcoa() Return a 2D/3D scatter plot for dimensionality reduction through PCoA
 dimred_umap() Return a 2D/3D scatter plot for dimensionality reduction through UMAP
 dimred_tsne() Return a 2D/3D scatter plot for dimensionality reduction through t-SNE
Alpha and beta diversity
 diversities() Return alpha diversity
 do_alpha_div_test() Compute various statistical tests for alpha diversity
 alpha_div_boxplot() Generate box plots comparing alpha diversity across groups of samples
 diversity_beta_test() Compute various statistical tests for beta diversity
 diversity_beta_boxplot() Generate box plots comparing beta diversity across groups of samples
 diversity_beta_heatmap() Generate a heatmap comparing beta diversity across groups of samples
Differential abundance analysis
 differential_abundance() Performs differential abundance analysis across groups of samples
Biomarker discovery
 find_biomarker() Identifies microbes as potential biomarkers for groups of samples