Man pages for vallenderlab/MicrobiomeR
Analyze Microbiome Data
| agglomerate_taxmap | Agglomerate taxmap Objects |
| alpha_diversity_measures | Alpha Diversity Measures |
| alpha_diversity_plot | Alpha Diversity Plot |
| as_analyzed_format | As Analyzed MicrobiomeR Format |
| as_basic_format | As Basic MicrobiomeR Format |
| as_custom_format | As Custom MicrobiomeR Format |
| as_MicrobiomeR_format | As MicrobiomeR Format |
| as_phyloseq_format | As Phyloseq MicrobiomeR Format |
| as_raw_format | As Raw MicrobiomeR Format |
| combination_palette | Combine Color Palettes |
| convert_proportions | Convert Proportions |
| correlation_data | Get Correlation Plot Data |
| correlation_plot | Correlation Plot |
| correlation_plots | Get Multiple Correlation Plots |
| cov_filter | Coefficient of Variation Filter |
| create_phyloseq | Get Phyloseq Object |
| create_pub_table | Create Publication Table |
| create_taxmap | Get Taxmap Object |
| get_color_palette | Get a Color Palette |
| heat_tree_parameters | Get Heat Tree Parameters |
| heat_tree_plots | Get Heat Tree Plots |
| is_analyzed_format | Is Analyzed MicrobiomeR Format |
| is_basic_format | Is Basic MicrobiomeR Format |
| is_phyloseq_format | Is Phyloseq MicrobiomeR Format |
| is_raw_format | Is Raw MicrobiomeR Format |
| melt_taxmap | Melt Taxmap |
| metacoder_comp_func_1 | Metacoder Comparison Function #1 |
| MicrobiomeR | MicrobiomeR |
| MicrobiomeR_Formats | The MicrobiomeR Formats |
| MicrobiomeR_Workflow | The MicrobiomeR Workflow |
| order_metacoder_data | Order Metacoder Observation Data |
| ordination_plot | Ordination Plot |
| ordination_plots | Ordination Plots |
| otu_id_filter | Filter OTU Ids from Taxmap Objects |
| otu_prevalence_filter | OTU Prevalence Filter |
| otu_proportion_filter | OTU Proportion Filter |
| output_dir | Create an Output Directory |
| parse_taxonomy_silva_128 | Parse elements of a taxonomy vector |
| permanova | PERMANOVA |
| phyloseq_silva_2 | Phyloseq Data with 2 Treatment Groups |
| phyloseq_silva_3 | Phyloseq Data with 3 Treatment Groups |
| pick_new_outgroup | Pick Outgroup for Tree |
| pipe | Pipe operator |
| plot_limits | Get Plot Limits |
| raw_silva_2 | "raw_format" Data with 2 Treatment Groups |
| raw_silva_3 | "raw_format" Data with 3 Treatment Groups |
| root_by_longest_edge | Root Phylogenetic Tree |
| root_phyloseq_tree | Root phyloseq tree. |
| sample_id_filter | Filter Samples Ids from Taxmap Objects |
| save_alpha_diversity_plots | Save Alpha Diversity Plots |
| save_correlation_plots | Save Correlation Plots |
| save_heat_tree_plots | Save Heat Tree Plots |
| save_ordination_plots | Save Ordination Plots |
| save_stacked_barplots | Save Stacked Barplots |
| save_top_coefficients_barplot | Save Top Coefficients Barplot |
| scico_palette | Scico Palette Function |
| stacked_barplot | Stacked Barplot |
| stacked_barplots | Stacked Barplots |
| taxa_prevalence_filter | Taxonomic Prevalence Filter (Metacoder) |
| taxon_id_filter | Filter Taxon Ids from Taxmap Objects |
| top_coefficients_barplot | Top Coefficients Barplot |
| transformer | Transforming Tidy Data |
| transposer | Transposing Tidy Data |
| treatment_matrix | Get Treatment Matrix |
| validate_MicrobiomeR_format | Validate MicrobiomeR Format |
| viridis_magma_palette | Viridis-Magma Palette Function |
| viridis_palette | Viridis Palette Function |
| vlookup | Mock Excel "VlookUp" Function |
| which_format | Which MicrobiomeR Format |
