| format_phyloseq | Formatting the 'phyloseq-class' Object |
| format_to_besthit | Formatting the 'phyloseq-class' Object advanced |
| get_microbiome_data | Download test microbiome data |
| list_microbiome_data | List of available datasets |
| microbiome_pipeline | Microbiome analysis pipeline |
| percent_classified | Summarize the percent taxa classification for 'phyloseq-class' |
| phy_to_ldf | Convert 'phyloseq-class' object to long data format |
| plot_alpha_diversities | Creat a plot for alpha diversities calculated using the 'microbiome' package |
| plot_ordination_utils | Plot species loading with ordinations |
| plot_ordiplot_core | Plotting core microbiota on ordinations |
| plot_read_distribution | Distribution of reads |
| plot_select_taxa | A boxplot for user specified list of taxa |
| plot_taxa_boxplot | Taxonomic Composition Plot boxplot |
| plot_taxa_composition | Taxonomic Composition Plot |
| plot_taxa_cv | Coefficient of variations |
| plot_taxa_heatmap | Heatmap using 'phyloseq-class' and 'pheatmap' |
| print_ps | Overview of 'phyloseq-class' |
| taxa_summary | Give taxa summary at specified taxonomic level |
| zackular2014 | Test data |