KEGG_gather             Gather metadata from KEGG for metabolites
PCA_plot                Create a PCA plot
assign_hierarchy        Assign hierarchy metadata
c57_nos2KO_mouse_countDF
                        c57b6J nos2KO metabolomics count matrix
c57_nos2KO_mouse_metadata
                        c57b6J nos2KO meta data
check_zeros             Check data for zeros across samples within
                        factor levels. Will determine if there are more
                        zeros than a user specified threshold within
                        any given factor level(s). Returns a vector of
                        Metabolites that are 0 above the threshold in
                        any given factor level.
count_fold_changes      Get counts for significant fold changes by
                        metabolite class.
get_seqs                Get nucleotide and amino acid sequences for
                        genes
make_omelette           Get metadata from KEGG API
omu_anova               Perform anova
omu_summary             omu_summary Performs comparison of means
                        between two independent variables, standard
                        deviation, standard error, FDR correction, fold
                        change, log2FoldChange. The order effects the
                        fold change values
pie_chart               Create a pie chart
plate_omelette          plate_omelette Internal method for KEGG_Gather
                        which parses flat text files
plate_omelette_rxnko    Clean up orthology metadata
plot_bar                Create a bar plot
plot_boxplot            Create a box plot
plot_heatmap            Create a heatmap
plot_rf_PCA             plot_rf_PCA
plot_variable_importance
                        plot_variable_importance
plot_volcano            Create a volcano plot
ra_table                Creates a ratio table from the
                        count_fold_changes function output.
random_forest           random_forest Perform a classification or
                        regression random forest model
read_metabo             Import a metabolomics count data frame
transform_metabolites   transform_metabolites
transform_samples       transform_samples
