.checkfile              check file format
.getstar                replace p value with star
.lda.fun                LEfse function
betadiv                 calcaute beta diversity
betatest                PERMANOVA test for phyloseq
biomarker               Identify biomarker by using randomForest method
buildTree               contruction of plylogenetic tree (extreme slow)
data-physeq             The physeq data was modified from the (Data)
                        Global patterns of 16S rRNA diversity at a
                        depth of millions of sequences per sample
                        (2011)
difftest                Calculate differential bacteria with DESeq2
distcolor               distinguish colors for making figures
do_aov                  do anova test and return results as data.frame
do_ttest                do t.test
do_wilcox               do wilcox test
glmr                    Do the generalized linear model regression
ldamarker               Identify biomarker by using LEfSe method
lightcolor              light colors for making figures
normalize               Normalize the phyloseq object with different
                        methods
otu_table               extract otu table
phy_tree                Retrieve phylogenetic tree (phylo-class) from
                        object.
plotLDA                 plot LEfSe results from ldamarker function
plotalpha               plot alpha diversity
plotbar                 plot bar for relative abundance for bacteria
plotbeta                plot beta diversity
plotdiff                plot differential results
plotmarker              plot the biomarker from the biomarker function
                        with randomForest
plotquality             plot the quality for the fastq file
preRef                  Download the reference database
prefilter               filter the phyloseq
processSeq              Perform dada2 analysis
psmelt                  Melt phyloseq data object into large data.frame
richness                calculat the richness for the phyloseq object
sample_data             extract sample information
subset_samples          Subset the phyloseq based on sample
subset_taxa             Subset species by taxonomic expression
tax_table               extract taxonomy table
