Package index
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add_taxonomy_prefix() - Add taxonomic prefixes to tax_table columns
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agglomerate_taxa() - Agglomerate Taxa by Taxonomic Rank
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check_taxonomic_consistency() - Check Taxonomic Consistency Across Higher-Level Classifications
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filter_features() - Filter Features Based on Abundance and Prevalence
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get_presence_list() - Get a List of Present Taxa by Group
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get_taxa_overlaps() - Compute Taxa Overlaps and Specific Sets Across Groups
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info()`info<-`()infoKeys()infoFields()taxrank()`taxrank<-`()transforms()`transforms<-`()mpa_version(<microEDA>)`mpa_version<-`(<microEDA>)filtered_taxa()`filtered_taxa<-`()filter_history()`filter_history<-`() - Get or set the info slot from a microEDA object
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join_mpa_profiles() - Join multiple MetaPhlAn profiles
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load_metaphlan() - Load a MetaPhlAn taxonomic profile from a file
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merged_metaphlan_profiles - Merged MetaPhlAn4 profiles data
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metaphlanProfile-class - A class to represent a MetaPhlAn profile
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microEDA()show(<microEDA>) - A S4 class extending phyloseq for microbiome data analysis
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mpa_taxProfile()`mpa_taxProfile<-`() - Get or set the MetaPhlAn taxonomic profile
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mpa_version()`mpa_version<-`() - Get or set the MetaPhlAn database version.
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`otu_table<-`(<microEDA>,<otu_table>) - Replace OTU table in a microEDA object
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`phy_tree<-`(<microEDA>,<phylo>) - Replace phylogenetic tree in a microEDA object
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plot_taxa_barchart() - Plot Taxonomic Composition of a microEDA/phyloseq Object
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plot_taxa_heatmap() - Plot heatmap of taxon abundance or prevalence
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plot_taxa_sankey() - Create a Sankey Plot of Taxonomic Abundances
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plot_taxa_upset() - Create an UpSet Plot of Shared and Unique Taxa
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`sample_data<-`() - Replace sample data in a microEDA object
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show_filter_history() - Display Filter History for a microEDA Object
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single_metaphlan_profile - SRS014476-Supragingival_plaque data
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summary(<microEDA>) - Summarize a microEDA object
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`tax_table<-`(<microEDA>,<taxonomyTable>) - Replace taxonomic table in a microEDA object
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to_phyloseq() - Convert an object to a phyloseq object
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trim_taxonomy_prefix() - Remove taxonomic prefixes from tax_table columns