Man pages for mikemc/speedyseq
Faster implementations of phyloseq functions
| as_tibble-phyloseq | Coerce phyloseq objects to tibble data frames |
| bad_flush_right | Replace all values with NA upon seeing a bad value |
| bad_or_unique | Reduce a vector x to its unique value or the value of 'bad' |
| filter-phyloseq | Subset rows in the taxonomy table or sample data using column... |
| filter_taxa | Filter taxa based on across-sample OTU abundance criteria |
| import_phyloseq_functions | Import phyloseq functions |
| join-phyloseq | Mutating joins of the taxonomy table or sample data |
| merge_groups | Merge groups of elements within a vector by a function |
| merge_samples2 | Merge samples by a sample variable or factor |
| merge_taxa_vec | Merge taxa in groups (vectorized version) |
| merge_taxa_vec_pseudo | Pseudo-merge taxa in groups |
| mutate-phyloseq | Create, modify, and delete columns in the taxonomy table or... |
| oneline | One-line summaries of phyloseq components |
| orient_taxa | Orient a phyloseq object or otu table to have taxa as rows or... |
| pipe | Pipe operator |
| plot_bar | A flexible, informative barplot phyloseq data |
| plot_heatmap | Create an ecologically-organized heatmap using ggplot2... |
| plot_tree | Plot a phylogenetic tree with optional annotations |
| psmelt | Melt phyloseq data object into large data.frame |
| reexports | Objects exported from other packages |
| relocate-phyloseq | Change column order in the taxonomy table or sample data |
| rename-phyloseq | Rename columns in the taxonomy table or sample data |
| sample_data_stable | Create sample data without adjusting row/sample names |
| select-phyloseq | Subset columns in the taxonomy table or sample data using... |
| select_taxa-methods | Select a subset of taxa in a specified order where possible |
| show-methods | Methods for 'show()' for phyloseq objects. |
| tax_glom | Agglomerate taxa using taxonomy. |
| tibble-constructors | Construct phyloseq objects from tibbles |
| tibble_print | Print a 2-d data.frame or matrix like a tibble |
| tip_glom | Agglomerate taxa using phylogeny-derived distances. |
| transform_sample_counts | Transform abundance data in an 'otu_table', sample-by-sample |
| tree_glom | Agglomerate taxa at a given phylogenetic resolution. |
| unique_or_na | Get the unique value in x or NA if none |
