PrepRecipe-class        PrepRecipe-class object
abundance_plt           Abundance boxplot
add_tax                 Adds taxonomic level of interest in the Recipe.
add_var                 Adds variable of interest to the Recipe
bake                    Define consensus strategies from a Recipe
contains_rarefaction    Checks if Recipe contains a rarefaction step
cool                    Extract results from defined bake
corr_heatmap            Plot otuput of the 'overlap_df' function as a
                        heatmap.
exclusion_plt           Plot the number of shared DA OTUs between
                        methods.
export_steps            Export step parameters as json.
find_intersections      Finds common OTU between method results
get_phy                 Returns phyloseq from Recipe-class object
get_tax                 Returns tax_info from Recipe-class object
get_var                 Returns var_info from Recipe-class object
import_steps            Import steps from json file
intersection_df         Returns data.frame with OTU intersection
                        between methods
intersection_plt        Plot results using UpSet plot
metaHIV_phy             Phyloseq object from metaHIV project
mutual_plt              Mutual finding plot
otu_table               Extracts otu_table from phyloseq inside a
                        Recipe
overlap_df              Overlap of significant OTUs between tested
                        methods.
phy_qc                  Phyloseq Quality Control Metrics
phyloseq_or_null-class
                        Recipe-class object
prep                    Performs all the steps defined in a Recipe
rand_id                 Make a random identification field for steps
recipe                  Create a Recipe for preprocessing data
sample_data             Extracts sample_data from phyloseq inside a
                        Recipe
step_aldex              ALDEx2 analysis
step_corncob            corncob analysis
step_deseq              DESeq2 analysis
step_filter_by_abundance
                        Filter taxa by abundance
step_filter_by_prevalence
                        Filter taxa by prevalence
step_filter_by_rarity   Filter taxa by rarity
step_filter_by_variance
                        Filter taxa by variance
step_filter_taxa        Filter taxa based on across-sample OTU
                        abundance criteria
step_lefse              lefse analysis
step_maaslin            MaAsLin2 analysis
step_metagenomeseq      MetagenomeSeq analysis
step_rarefaction        Resample an OTU table such that all samples
                        have the same library size.
step_subset_taxa        Subset taxa by taxonomic level
step_wilcox             Wilcox analysis
steps_ids               Get step_ids from recipe
tax_table               Extracts tax_table from phyloseq inside a
                        Recipe
test_prep_rec           PrepRecipe for metaHIV_phy data
test_rec                Recipe for metaHIV_phy data
zero_otu                Extract outs with all 0 values in at least on
                        level of the variable
