Man pages for kstagaman/phyloseqCompanion
Provides additional functions to work with phyloseq objects
| clr.transform | Center Log Ratio tranform phyloseq |
| example_phyloseq | A simple phyloseq object |
| gen.dist.matrices | Generate Distance Matrices |
| get.biplot.data | Extract CCA/RDA biplot data |
| hello | Hello, World! |
| numbered.ASVs | Numbered ASVs |
| numberedASVs_phyloseq | A phyloseq object with numbered ASVs |
| otu.data.table | otu_table to data.table |
| otu.matrix | otu_table to matrix |
| phyloseq2lefse | Phyloseq to LefSe |
| prep.physeq | Prepare a phyloseq with raw counts for analysis |
| remove.euks | Remove eukaryotic taxa from a phyloseq object |
| rename.NA.taxa | rename NA taxonomic levels |
| sample.data.frame | sample_data to data.frame |
| sample.data.table | sample_data to data.table |
| taxa.data.table | tax_table to data.table |
| taxa.matrix | tax_table to matrix |
| taxa.prevalence | get prevalence (presence in number of samples) for each taxon |
