alpha_div_boxplot       Alpha diversity boxplot
alpha_div_test          Get alpha diversity
counts_to_logcpm        Covert a counts table to a relative abundances
                        table
counts_to_relabu        Covert a counts table to a relative abundances
                        table
df_char_to_factor       Factorize all categorical columns
differential_abundance
                        Differential abundance analysis
dimred_pca              Dimensionality reduction through PCA
dimred_pcoa             Dimensionality reduction through PCoA
dimred_tsne             Dimensionality reduction through t-SNE
dimred_umap             Dimensionality reduction through PCA
diversities             Get alpha diversity
diversities_help        Get alpha diversity
diversity_beta_NMDS     Beta diversity NMDS plot
diversity_beta_boxplot
                        Beta diversity boxplot
diversity_beta_heatmap
                        Beta diversity heatmap
diversity_beta_test     Perform a beta diversity test
do_alpha_div_test       Alpha diversity statistical test
filter_categorize       Categorize continuous variables
filter_summary_bar_density
                        Data visualization by bar plot / density plot
filter_summary_pie_box
                        Data visualization by pie chart / box plot
find_biomarker          Identify biomarkers
find_taxon_mat          Find the Taxonomy Information Matrix
find_taxonomy           Find the taxonomy for unlimited tids
find_taxonomy_300       Find the taxonomy for maximum 300 tids
gini_simpson            Get alpha diversity using gini
grep_tid                Greps the tid from the given identifier string
inverse_simpson         Get alpha diversity using inverse simpson
is_categorical          Check if object is categorical
is_integer0             check if integer(0)
is_integer1             check if integer(1)
mae_pick_organisms      Modify organisms of multi-assay experiment
                        object
mae_pick_samples        Modify samples of multi-assay experiment object
pct2str                 Converts decimal percentage to string with
                        specified digits
percent                 Format decimals to percentages
read_pathoscope_data    Reads the data from PathoScope reports and
                        returns a list of final guess relative
                        abundance and count data
relabu_barplot          Plot bar plots of sample and group level
                        relative abundance
relabu_boxplot          Plot boxplots comparing different organism
                        prevalence across conditions
relabu_heatmap          Plot heatmap of sample level counts in logcpm
run_animalcules         Run animalcules shiny app
shannon                 Get alpha diversity using shannon
simpson_index           Get alpha diversity using simpson
upsample_counts         Upsample a counts table to a higher taxon level
write_to_biom           Output biom
