Man pages for microsud/microbiomeutilities
microbiomeutilities: Utilities for Microbiome Analytics
| add_refseq | Add refseq slot for dada2 based phyloseq object |
| aggregate_top_taxa2 | Aggregate Top Taxa v2 |
| dominant_taxa | Dominant Taxa |
| find_samples_taxa | Find samples dominated by specific taxa |
| format_to_besthit | Formatting the 'phyloseq-class' Object advanced |
| get_group_abundances | Taxa abundance summary by group |
| get_microbiome_data | Download test microbiome data |
| get_tibble | Convert Phyloseq Slots to Tibbles |
| hmp2 | Test data 2 |
| join_otu_tax | Join otu_table and tax_table to Tibble |
| list_microbiome_data | List of available datasets |
| make_pairs | Make pairs |
| peak-methods | Peak into 'phyloseq' objects |
| percent_classified | Summarize the percent taxa classification for... |
| phy_to_ldf | Convert 'phyloseq-class' object to long data format |
| plasticity | Plasticity |
| plot_abund_prev | Mean Abundance-Prevalence relation |
| plot_alpha_diversities | Creat a plot for alpha diversities calculated using the... |
| plot_alpha_rcurve | Rarefaction curves for alpha diversity indices |
| plot_area | Area plot |
| plot_diversity_stats | Diversity plot with stats |
| plot_listed_taxa | A boxplot for user specified list of taxa |
| plot_ordination_utils | Plot species loading with ordinations |
| plot_ordiplot_core | Plotting core microbiota on ordinations |
| plot_paired_abundances | A paired-boxplot for user specified list of taxa |
| plot_read_distribution | Distribution of reads |
| plot_select_taxa | A boxplot for user specified list of taxa |
| plot_spaghetti | Spaghetti Plots |
| 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' |
| prep_ternary | Create table for Ternary plot |
| prep_tern_otu | Create table for ternary plot OTU |
| print_ps | Overview of 'phyloseq-class' |
| rarefy_util | #@param mat otu table rows as taxa names #@param names_fun... |
| simple_heatmap | Simple Heatmap |
| taxa_distribution | Distribution of taxa |
| taxa_pooler_mcola | Pool Taxa |
| taxa_summary | Give taxa summary at specified taxonomic level |
| theme_biome_utils | Custom theme for microbiomeutilities pkg |
| zackular2014 | Test data |
