Man pages for cpauvert/psadd
Additions to phyloseq package for microbiome analysis
| adaptative_threshold_otu | Relevel taxa/OTU to 0 according to a taxa/OTU wise threshold. |
| ctrl_samples_stats | Generate taxa/OTU statistics to compare control samples with... |
| get_taxa_nomy | Taxa/OTU abundance in a given sample coupled with rank and... |
| id2hash | Convert taxa/ID through a correspondence table |
| multiple_rrarefy | Performs rarefying multiple times and returns averaged OTU... |
| plot_krona | Interactive Taxonomy plot with Krona from a phyloseq object |
| plot_mv | Plot Mean Variance OTU in order to evaluate overdispersion |
| plot_pie | Pie Plot Taxonomy Assignations from Phyloseq |
| plot_pie_vector | Pie Plot Taxonomy Assignations from Two Abundance Vector |
| plot_pie_with_legend | Plot Taxonomy Assignations from Phyloseq with legend. |
| plot_sparsity | Plot taxa/OTU table to evaluate sparsity. |
| plot_violin | Violin distribution plot |
| relative_abd_without_specific_sample | Compute taxa/OTU abundance relative to the total dataset |
| relative_abundance | Compute taxa/OTU abundance relative to the total dataset |
| rename_otu | OTU renaming: from hash to rank abundance prefix |
| sample_prev | Taxa/OTU number in all samples |
| sample_stats | Apply statistics function to samples. |
| subset_samples_no_zero | Subset samples and prune taxa/OTU with zero abundance |
| taxa_prev | OTU/Species prevalence in all samples |
| taxa_stats | Apply statistics function to taxa abundance vector |
