Package index • microbiomedataset

Core object

create_microbiome_dataset(): create_microbiome_dataset

update_microbiome_dataset(): Upgrade a microbiome_dataset Object to the Current Schema

microbiome_dataset-class: microbiome_dataset class

activate_microbiome_dataset(): Activate a Specific Component of a Microbiome Dataset

check_microbiome_dataset(): Validate the Format and Consistency of a Microbiome Dataset

check_microbiome_dataset_class(): Check Integrity and Structure of Microbiome Dataset Object

Import and conversion

convert2MPSE() as.MPSE(): convert to MPSE class object.

convert2TreeSummarizedExperiment() as.TreeSummarizedExperiment(): convert to TreeSummarizedExperiment class object.

convert2mass_dataset() as.mass_dataset(): convert to mass_dataset class object.

convert2microbiome_dataset() as.microbiome_dataset(): convert to microbiome_dataset class object.

convert2phyloseq() as.phyloseq(): convert to phyloseq class object.

convert2tbl_graph() as.tbl_graph(): convert to tbl_graph class object in tidygraph.

convert2treedata() as.treedata(): convert data.frame contained hierarchical relationship or other classes to treedata class

align_ref_seq(): Align Reference Sequences with the Current Dataset

align_tree(): Align a Tree Slot with the Current Dataset

import_biom(): Import a BIOM Table as a microbiome_dataset

import_dada2(): Import DADA2-style Outputs as a microbiome_dataset

import_qiime2(): Import a QIIME2 Dataset as a microbiome_dataset

import_tree(): Import a Tree from Newick into a Microbiome Dataset

export_tree(): Export a Tree Slot to Newick or Nexus

import_ref_seq(): Import Reference Sequences from FASTA

export_ref_seq(): Export Reference Sequences to FASTA

replace_tree(): Replace a Tree Slot in a Microbiome Dataset

replace_ref_seq(): Replace Reference Sequences in a Microbiome Dataset

prune_tree(): Prune a Tree Slot in a Microbiome Dataset

prune_ref_seq(): Prune Reference Sequences in a Microbiome Dataset

filter_tree_by_rank(): Filter the Taxa Tree by a Taxonomic Rank

Manipulation

left_join_microbiome_dataset(): Left join for microbiome_dataset

mutate2sample(): Mutate new columns into sample_info

mutate2variable(): Mutate New Columns into Variable Info of Microbiome Dataset

prune_samples(): Prune Samples from a Microbiome Dataset

prune_taxa(): Prune Taxa from a Microbiome Dataset

filter_samples(): Filter Samples by Library Size

filter_taxa(): Filter Taxa by Abundance or Prevalence

filter_samples_by_group(): Filter Samples by a Sample Metadata Group

filter_taxa_by_rank(): Filter Taxa by a Taxonomic Rank

merge_samples(): Merge Samples by a Sample Metadata Column

summarise_samples() summarize_samples(): Summarize Samples in a Microbiome Dataset

summarise_samples_by_group(): Summarise Samples by a Sample Metadata Group

summarise_taxa(): Summarise Taxa at a Taxonomic Rank

summarise_variables() summarize_variables(): merge samples

agglomerate_taxa(): Agglomerate Taxa to a Taxonomic Rank

agglomerate_tree(): Agglomerate Taxa Using Tree Distances

sample_sums(): Calculate Total Abundance per Sample

taxa_sums(): Calculate Total Abundance per Taxon

taxa_prevalence(): Calculate Taxon Prevalence across Samples

transform_counts(): Transform Count Data in a Microbiome Dataset

transform2relative_intensity(): transform data to relative data

transform_taxa(): Transform Taxa after Taxonomic Summarization

transform_samples(): Transform Samples after Sample Group Summarization

transform_abundance_by(): Transform Abundance by Taxa or Sample Groups

summarise_abundance(): Summarise Abundance by Taxa or Sample Groups

Extraction and visualization

extract_otu_tree() extract_taxa_tree() extract_ref_seq(): extract_otu_tree

extract_association_result(): Extract Cross-Omics Association Results

extract_correlation_table(): Extract a Tidy Correlation Table

extract_crossomics_integration(): Extract Cross-Omics Integration Result

extract_crossomics_matrix(): Extract Matched Cross-Omics Matrices

extract_differential_abundance_result(): Extract Differential Abundance Results

extract_diversity_result(): Extract Diversity Results

extract_intensity(): extract_intensity

extract_mechanism_result(): Extract Mechanism Results

extract_network_result(): Extract Network Results

extract_network_table(): Extract Network Tables

extract_ordination_result(): Extract Ordination Coordinates

extract_tree_data(): Extract Tree Data from a Microbiome Dataset

extract_tree_link_data(): Extract Tree Link Metadata

extract_longitudinal_mixed_effect_result() as_tibble_longitudinal_mixed_effect() create_longitudinal_mixed_effect_result() plot_longitudinal_mixed_effect() plot_longitudinal_effect_heatmap(): Extract Longitudinal Mixed-Effect Results

melt_crossomics_features(): Melt Matched Cross-Omics Features

melt_features(): Melt Features into a Long Table

melt_taxa(): Melt Taxa into a Rank-level Long Table

melt_tree(): Melt a Tree Slot into a Tidy Table

check_tree_link(): Check Explicit Tree Link Metadata

plot_composition(): Plot Microbiome Composition

plot_abundance(): Plot Taxon Abundance

plot_abundance_density(): Plot Abundance Density

plot_richness(): Plot Multiple Alpha Diversity Metrics

plot_heatmap(): Plot a Microbiome Heatmap

plot_heatmap_annotation(): Plot a Heatmap with Metadata Annotations

plot_prevalence(): Plot Taxon Prevalence

plot_prevalence_abundance(): Plot Prevalence versus Abundance

plot_core_taxa(): Plot Core Taxa

plot_taxa_boxplot(): Plot Taxa as Boxplots

plot_taxa_violin(): Plot Taxa as Violin Plots

plot_sample_depth(): Plot Sample Depth

plot_rarefaction(): Plot Alpha Rarefaction Curves

plot_distance_heatmap(): Plot a Distance Heatmap

plot_scree(): Plot an Ordination Scree Plot

plot_tree_link(): Plot Tree Link Coverage

psmelt_microbiome_dataset(): Melt a microbiome_dataset into a Long Table

psmelt_taxa(): Melt Taxonomic Abundance into a Long Table

plot_barplot(): Barplot based on ggplot2

plot_tree(): Plot a Tree Slot from a Microbiome Dataset

plot_tree_abundance(): Plot Tree Abundance

plot_tree_interactive(): Plot an Interactive Tree

plot_tree_heatmap(): Plot a Tree-Ordered Heatmap

plot_longitudinal(): Plot Longitudinal Taxa Trajectories

plot_taxa_overlap(): Plot Taxa Overlap Between Groups

plot_prevalence_upset(): Plot Prevalence UpSet

plot_taxonomy_sunburst(): Plot Taxonomy as a Sunburst

plot_alpha_diversity(): Plot Alpha Diversity

plot_beta_diversity(): Plot Beta Diversity

plot_ordination(): Plot Ordination Results

plot_ordination_biplot(): Plot an Ordination Biplot

plot_ordination_3d(): Plot a 3D Ordination

plot_correlation_heatmap(): Plot a Correlation Heatmap

plot_correlation_dotplot(): Plot Correlations as a Dotplot

plot_network_modules(): Plot Network Modules

plot_network_centrality(): Plot Network Centrality

plot_module_composition(): Plot Module Composition

plot_module_summary(): Plot a Network Module Summary

build_mechanism_network(): Build a Mechanism Network

plot_mechanism_network(): Plot a Mechanism Network

plot_mechanism_summary(): Plot a Mechanism Summary

calculate_pathway_enrichment(): Calculate Pathway Enrichment from Mechanism Links

plot_pathway_enrichment(): Plot Pathway Enrichment

plot_pathway_summary(): Plot a Pathway Summary

create_differential_abundance_result(): Create a Differential Abundance Result Object

run_differential_abundance(): Run Differential Abundance Analysis

mixed_effect_result_class longitudinal_mixed_effect_result-class longitudinal_mixed_effect_result: longitudinal_mixed_effect_result class

as_tibble_association(): Convert Association Results to a Tibble

as_tibble_network(): Convert Network Results to a Tibble

as_tibble_crossomics_integration(): Convert Cross-Omics Integration Results to Tibbles

as_tibble_mechanism(): Convert Mechanism Results to a Tibble

as_tibble_differential_abundance(): Convert Differential Abundance Results to a Tibble

plot_differential_ma(): Plot a Differential Abundance MA Plot

plot_differential_heatmap(): Plot a Differential Abundance Heatmap

plot_differential_boxplot(): Plot Differential Taxa as Boxplots

plot_differential_volcano(): Plot a Differential Abundance Volcano Plot

plot_differential_effect_size(): Plot Differential Effect Sizes

plot_differential_cladogram(): Plot a Differential Abundance Cladogram

Package data and utilities

global_patterns: Global Patterns of 16S rRNA Diversity

demo_crossomics: Paired Microbiome-Metabolome Demo Data

get_microbiomedataset_version(): Retrieve the Version of the microbiomedataset Package

microbiomedataset_conflicts(): Conflicts between the microbiomedataset and other packages

microbiomedataset_logo(): Display Logo and Version Information for microbiomedataset

microbiomedataset_packages(): List all packages in the microbiomedataset

Analysis

calculate_alpha_diversity(): Calculate Alpha Diversity

calculate_beta_diversity(): Calculate Beta Diversity

run_ordination(): Run Ordination on a Microbiome Dataset

microbiome_diversity-class: microbiome_diversity class

microbiome_ordination-class: microbiome_ordination class

as_tibble_diversity(): Convert Diversity Results to a Tibble

as_tibble_ordination(): Convert Ordination Results to a Tibble

Cross-omics integration

create_microbiome_metabolome_dataset(): Create a Joint Microbiome-Metabolome Dataset

check_crossomics_dataset(): Check a Joint Microbiome-Metabolome Dataset

align_samples_between_omics(): Align Samples Between Microbiome and Metabolome Data

extract_crossomics_matrix(): Extract Matched Cross-Omics Matrices

melt_crossomics_features(): Melt Matched Cross-Omics Features

prepare_correlation_data(): Prepare Matched Data for Correlation Analysis

calculate_correlation() calculate_correlation_spearman() calculate_correlation_pearson() calculate_correlation_sparcc(): Calculate Microbe-Metabolite Correlations

extract_correlation_table(): Extract a Tidy Correlation Table

filter_correlation(): Filter Correlation Results

build_correlation_network(): Build a Microbe-Metabolite Correlation Network

extract_network_table(): Extract Network Tables

convert_network_graph(): Convert a Correlation Network to tbl_graph

calculate_network_centrality(): Calculate Network Centrality

detect_network_modules(): Detect Network Modules

summarise_network_modules(): Summarize Network Modules

plot_correlation_network(): Plot a Correlation Network

associate_microbe_metabolite(): Associate Microbiome Taxa with Metabolites

integrate_microbe_metabolite(): Integrate Matched Microbiome and Metabolome Data

plot_crossomics_integration(): Plot Cross-Omics Integration

plot_crossomics_loading_heatmap(): Plot Cross-Omics Loading Heatmap

plot_crossomics_network(): Plot Cross-Omics Feature Network

extract_crossomics_integration(): Extract Cross-Omics Integration Result

infer_metabolic_link(): Infer Mechanistic Microbe-Metabolite Links

standardize_metabolite_annotation(): Standardize Metabolite Annotation

standardize_pathway_link(): Standardize Pathway Link Metadata

standardize_reaction_link(): Standardize Reaction Link Metadata

standardize_taxon_pathway_link(): Standardize Taxon-to-Pathway Link Metadata

standardize_taxon_reaction_link(): Standardize Taxon-to-Reaction Link Metadata

summarise_pathways(): Summarize Pathway-Level Mechanisms

summarise_reactions(): Summarize Reaction-Level Mechanisms

microbiome_metabolome_dataset-class: microbiome_metabolome_dataset class

microbe_metabolite_association-class: microbe_metabolite_association class

microbe_metabolite_network-class: microbe_metabolite_network class

differential_abundance_result-class: differential_abundance_result class

crossomics_mechanism-class: crossomics_mechanism class

crossomics_integration-class: crossomics_integration class