Man pages for microsud/microbiomeutilities-shiny
microbiomeutilities: An R package with utility functions for the microbiome R package
| biogeogut | Comparison of small intestine and stool microbiota |
| format_phyloseq | Formatting the Phyloseq Object |
| format_to_besthit | Formatting the Phyloseq 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 |
| phy_to_ldf | Convert phyloseq object to long data format |
| plot_alpha_diversities | plot_alpha_diversities |
| plot_ordiplot_core | Plotting core microibota on ordinations |
| plot_ReadDistribution | Distribution of reads |
| plot_select_taxa | plot_select_taxa plot selected OTUs of interest |
| 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 and pheatmap |
| theme_mutilties | simple theme optimised for visual appeal and clarity |
