abundanceFit            abundanceFit
ani_distance            ani_distance
caseControlFit          caseControlFit
comp_ani_diff_and_posthoc_test
                        Compute the mean ANI differences for contigs
                        with an identity effect and perform posthoc
                        testing to establish support for each hit.
compute_eb_priors       Constructor for strainspy_priors using
                        empirical Bayes estimation
define_priors           Constructor for strainspy_priors using preset
                        or user defined priors
estimate_beta_diversity
                        Estimate beta diversity from ANI
estimate_sample_richness
                        Estimate species richness and coverage of
                        reference strains using ANI
extract_fixef_priors    Access fixef priors needed for ordinal beta
                        regression
extract_strainspy       Extract data from a StrainSpy
                        'SummarizedExperiment' object in long format
filter_by_presence      filter_by_presence
getContigNames          Get Contig names in a fit object
getGenomes              Get Genomes in a fit object
getPriorsDf             Access the prior specification table
getResiduals            Access Residuals
getSamples              Get Sample names in a fit object
getZICoefficients       Access Zero-Inflation Coefficients
glmObFit                glmObFit
glmQBFit                glmQBFit
glmZiBFit               glmZiBFit
hadjust                 Performs hierarchical taxonomy aware adjustment
                        of p-values.
merge_metaphlan_files   merge_metaphlan_files
merge_sourmash_files    merge_sourmash_files
merge_sylph_files       merge_sylph_files
modify_metadata         Add or modify metadata in a
                        'SummarizedExperiment' object
plot_ani_dist           Generate a violin or box plot for a subset of
                        contigs for a categorical phenotype.
plot_histogram          Generate a histogram for a single contig for a
                        categorical phenotype.
plot_manhattan          Generate a strain Manhattan plot from a
                        strainspy_fit object
plot_mds                Plot MDS of ANI data
plot_pca_biplot         plot_pca_biplot
plot_prior_bootstrap    Plot the bootstrap distributions behind a
                        strainspy_priors object
plot_volcano            Generate a Volcano Plot from a strainspy_fit
                        Object
prep_for_prediction     Prepare a caret-compatible prediction data
                        frame from a SummarizedExperiment
read_metaphlan          read_metaphlan
read_sourmash           read_sourmash
read_sylph              Read Sylph query or profile output file and
                        create a SummarizedExperiment object
read_taxonomy           Read and process a taxonomy file
show,strainspy_fit-method
                        Show Method for strainspy_fit
show,strainspy_priors-method
                        Show method for strainspy_priors objects
strainspy               Strainspy Wrapper
strainspy_fit-accessors
                        Accessors for strainspy_fit objects
strainspy_fit-class     strainspy_fit: A Class for storing fit data
                        from all strainspy models
strainspy_priors-class
                        strainspy_priors: A Class for storing model
                        fitting priors
summary,strainspy_fit-method
                        Summary Method for strainspy_fit
top_hits                Provides the top results of a strainspy_fit
                        object, sorted by adjusted p-value.
