Man pages for microbiome
Microbiome Analytics
| abundances | Abundance Matrix from Phyloseq |
| aggregate_rare | Aggregate Rare Groups |
| aggregate_taxa | Aggregate Taxa |
| aggregate_top_taxa | Aggregate Top Taxa |
| alpha | Global Ecosystem State Variables |
| associate | Cross Correlation Wrapper |
| atlas1006 | HITChip Atlas with 1006 Western Adults |
| baseline | Pick Baseline Timepoint Samples |
| bfratio | Bacteroidetes-Firmicutes Ratio |
| bimodality | Bimodality Analysis |
| bimodality_sarle | Sarle's Bimodality Coefficient |
| boxplot_abundance | Abundance Boxplot |
| chunk_reorder | Chunk Reorder |
| cmat2table | Convert Correlation Matrix into a Table |
| collapse_replicates | Collapse Replicate Samples |
| core | Core Microbiota |
| core_abundance | Core Abundance |
| core_heatmap | Core Heatmap |
| core_matrix | Core Matrix |
| core_members | Core Taxa |
| coverage | Coverage Index |
| default_colors | Default Colors |
| densityplot | Density Plot |
| dietswap | Diet Swap Data |
| divergence | Divergence within a Sample Group |
| diversities | Diversity Index |
| diversity | Diversity Index |
| dominance | Dominance Index |
| dominant | Dominant taxa |
| estimate_stability | Estimate Stability |
| evenness | Evenness Index |
| find_optima | Find Optima |
| gktau | gktau |
| global | Global Ecosystem State Variables |
| group_age | Age Classes |
| group_bmi | Body-Mass Index (BMI) Classes |
| heat | Association Heatmap |
| hitchip.taxonomy | HITChip Taxonomy |
| hotplot | Univariate Bimodality Plot |
| inequality | Gini Index |
| intermediate_stability | Intermediate Stability |
| is_compositional | Test Compositionality |
| log_modulo_skewness | Log-Modulo Skewness Rarity Index |
| low_abundance | Low Abundance Index |
| map_levels | Map Taxonomic Levels |
| merge_taxa2 | Merge Taxa |
| meta | Retrieve Phyloseq Metadata as Data Frame |
| microbiome-package | R package for microbiome studies |
| multimodality | Multimodality Score |
| neat | Neatmap Sorting |
| neatsort | Neatmap Sorting |
| overlap | Overlap Measure |
| peerj32 | Probiotics Intervention Data |
| plot_atlas | Visualize Samples of a Microbiota Atlas |
| plot_composition | Taxonomic Composition Plot |
| plot_core | Visualize OTU Core |
| plot_density | Plot Density |
| plot_frequencies | Plot Frequencies |
| plot_landscape | Landscape Plot |
| plot_regression | Visually Weighted Regression Plot |
| plot_taxa_prevalence | Visualize Prevalence Distributions for Taxa |
| plot_tipping | Variation Line Plot |
| potential_analysis | Bootstrapped Potential Analysis |
| potential_univariate | Potential Analysis for Univariate Data |
| prevalence | OTU Prevalence |
| quiet | Quiet Output |
| radial_theta | Radial Theta Function |
| rare | Rare Microbiota |
| rare_abundance | Rare (Non-Core) Abundance Index |
| rare_members | Rare Taxa |
| rarity | Rarity Index |
| read_biom2phyloseq | Read BIOM File into a Phyloseq Object |
| readcount | Total Read Count |
| read_csv2phyloseq | Read Simple OTU Tables into a Phyloseq Object |
| read_mothur2phyloseq | Read Mothur Output into a Phyloseq Object |
| read_phyloseq | Import phyloseq Data |
| remove_samples | Exclude Samples |
| remove_taxa | Exclude Taxa |
| richness | Richness Index |
| spreadplot | Abundance Spread Plot |
| summarize_phyloseq | Summarize phyloseq object |
| taxa | Taxa Names |
| time_normalize | Normalize Phyloseq Metadata Time Field |
| time_sort | Temporal Sorting Within Subjects |
| timesplit | Time Split |
| top | Identify Top Entries |
| top_taxa | Top Taxa |
| transform | Data Transformations for phyloseq Objects |
| write_phyloseq | Exporting phyloseq Data in CSV Files |
| ztransform | Z Transformation |
