Man pages for microbiota/amplicon
Statistics and visualization for microbiome data
| alpha_barplot | Plotting alpha diversity barplot for each group with anova... |
| alpha_boxplot | Plotting alpha diversity boxplot for each group with ANOVA... |
| alpha_rare_all | Plotting rarefaction curve for each sample or group |
| alpha_rare_curve | Plotting rarefaction curve for each group |
| alpha_sample_rare | Plotting sample rarefaction boxplot |
| beta_cpcoa | Plotting beta diversity scatter plot of Constrained PCoA |
| beta_cpcoa_dis | Plotting beta diversity scatter plot of Constrained PCoA |
| BetaDiv | Beta diversity plotting and statistics |
| beta_pcoa | Plotting beta diversity scatter plot |
| beta_pcoa_stat | Calculate beta diversity p-value by Adonis |
| compare | Difference comparison |
| format2lefse | Format otutab, metadata and taxonomy into LEfSe format |
| format2lefse2 | Format otutab, metadata and taxonomy into LEfSe format with... |
| format2maptree | Format feature table and taxonomy into maptree data |
| format2stamp | Format otutab and taxonomy into each level for STAMP |
| MicroTest | Beta diversity statistics by adonis/anosim/MRPP in all groups |
| pairMicroTest | Beta diversity statistics by adonis/anosim/MRPP in pair |
| RDA_CCA | RDA or CCA calculate |
| tax_circlize | Plotting circlize of taxonomy for groups or samples |
| tax_maptree | Plotting maptree of taxonomy |
| tax_stack_clust | Plotting cluster tree + stackplot of taxonomy samples and... |
| tax_stackplot | Plotting stackplot of taxonomy for groups or samples |
| tax_wordcloud | Wordcloud plot relative abundance of taxonomy |
