AcceptableRange         Acceptable Range Data
MG_shapes               Predefined Shape Vector for Plot Styling
Pre_processing_hashcodes
                        Pre-process phyloseq or TSE object based on
                        hashcodes
Pre_processing_species
                        Pre-process taxa in a phyloseq or TSE object by
                        merging ASVs/OTUs
Pre_processing_species_list
                        Preprocess and Merge Spike-in Species in a
                        Phyloseq or TSE Object
RandomForest_selected   Select Important ASVs/OTUs Using Random Forest
adjust_abundance_one_third
                        Adjust Abundance by a Custom Factor
adjusted_prevalence     Adjust Prevalence in a Microbiome Object
alluvial_plot           Generate an Alluvial Plot for Microbiome Data
calculate_list_average_scaling_factors
                        Calculate Sample-specific Average Scaling
                        Factors for Multiple Spike-in Groups
calculate_spikeIn_factors
                        Calculate Scaling Factors for Spiked Species in
                        Phyloseq or TSE Object
calculate_spike_percentage
                        Calculate Spike Percentage for Specified Taxa
                        in a Phyloseq or TSE Object
calculate_spike_percentage_list
                        Calculate Spike-in Percentage for Specified
                        Taxa
calculate_summary_stats_table
                        Calculate Summary Statistics Table
color_palette           Original, Extended, and Nature-Inspired Color
                        Palette Sequence
conclusion              Compute Summary Statistics for Spiked Species
convert_categorical_to_factors
                        Convert Categorical Columns to Factors in
                        Sample Data
convert_phyloseq_to_tse
                        Convert a 'phyloseq' Object to a
                        'TreeSummarizedExperiment'
convert_to_absolute_counts
                        Convert Relative ASV/OTU Counts to Absolute
                        Counts
convert_tse_to_phyloseq
                        Convert a 'TreeSummarizedExperiment' to a
                        'phyloseq' Object
create_directory        Create a Directory and Optionally Set as
                        Working Directory
create_list             Create a List from a Phyloseq or TSE Object
degree_network          Analyze and Visualize a Microbial Network
detect_common_asvs_taxa
                        Detect Common ASVs and Taxa from Multiple
                        Phyloseq or TSE Objects
extract_neighbors       Extract First and Second Neighbors of a Target
                        Node
filter_and_split_abundance
                        Filter and Split Abundance Data by Threshold
get_long_format_data    Convert a Phyloseq or TSE Object into a
                        Long-Format Data Frame
get_otu_table           Extract OTU Tax Metadata from Object
get_phy_tree            Extract Phylogenetic Tree
get_reference_seq       Extract Reference Sequences
get_sample_data         Extract Sample Data
get_sample_sums         Extract Sample Sums from Object
get_tax_table           Extract Taxonomy Table
gm_mean                 Calculate Geometric Mean
imbalance_calculate_list_average_scaling_factors
                        Calculate Per-Sample Scaling Factors for
                        Multiple Spike-in Groups
label                   Label Taxonomic Ranks by Hashcode
load_graphml            Load GraphML Without 'id' Conflicts
metadata_full           Metadata for Microbiome Samples
my_custom_theme         Custom ggplot2 Theme with Consistent Aesthetics
node_level_metrics      Compute and Visualize Node-Level Network
                        Metrics
norm.DESeq              DESeq Normalization with Pseudocount and
                        Integer Conversion
norm.Poisson            Poisson Normalization and Differential
                        Abundance Function
norm.QN                 Quantile Normalization (QN) for phyloseq object
norm.TC                 TC Normalization (Total Count Scaling)
norm.TMM                TMM Normalization (Trimmed Mean of M component)
norm.UQ                 UQ Normalization (Upper Quartile)
norm.clr                CLR Normalization (Centered Log-Ratio
                        Transformation)
norm.css                CSS Normalization (Cumulative Sum Scaling)
norm.med                Median Normalization
norm.rar                Rarefying
norm.rle                RLE Normalization (Relative Log Expression)
norm.tss                TSS Normalization (Total Sum Scaling)
normalization_set       Apply the Selected Normalization Method to the
                        Phyloseq and TSE Objects
perform_and_visualize_DA
                        Perform and Visualize Differential Abundance
                        Analysis with edgeR or DESeq2
physeq                  Example Phyloseq Object with Tree and Reference
                        Sequences
physeq_16SOTU           Example Phyloseq Object for 16S OTUs
physeq_ITSOTU           Example Phyloseq Object for ITS OTUs
plot_core_microbiome_custom
                        Plot Core Microbiome Prevalence Heatmap
                        (Phyloseq & TSE Compatible)
plot_spikein_tree_diagnostic
                        Spike-in Tree Diagnostic Plot
plotbar_abundance       Taxa Bar Plot Without Aggregation (Relative or
                        Absolute Abundance)
proportion_adj          Proportionally Adjust Abundance
quadrant_plot           Generate Custom Quadrant Plots for Node Metrics
random_subsample_WithReductionFactor
                        Random Subsampling with Reduction Factor
randomsubsample_Trimmed_evenDepth
                        Subsampling to an Equal Sequencing Depth
regression_plot         Create a Regression Plot with Faceting by Range
relativized_filtered_taxa
                        Filter Taxa from a Phyloseq or TSE Object Based
                        on Custom Thresholds
remove_zero_negative_count_samples
                        Remove Samples with Zero, Negative Counts, or
                        NA Values and Add Pseudocount
ridge_plot_it           Generate Ridge Plots for Taxonomic Abundance
                        Distribution
set_nf                  Set Normalization Factors in the Sample Data of
                        the Phyloseq Object
simulate_network_robustness
                        Simulate Network Robustness under Node Removal
summ_ASV_OTUID          Summarize ASV Data Based on ASV_ID
summ_count_phyloseq     Summary Statistics of a Phyloseq or TSE Object
summ_phyloseq_sampleID
                        Generate Summary Statistics for Each Sample
taxa_barplot            Generate a Taxa Barplot with Relative or
                        Absolute Abundance
tidy_phyloseq_tse       Tidy a Phyloseq or TreeSummarizedExperiment
                        Object
tse                     Example TreeSummarizedExperiment (TSE) Object
                        with Tree and Reference Sequences
validate_spikein_clade
                        Validate Spike-In Clade Consistency with NJ
                        Tree and Bootstrap
weight_Network          Analyze and Visualize a Microbial Network
