alphasample-class       alphasample class
as.data.frame.diffAnalysisClass
                        get the table of diffAnalysisClass
build_tree              building tree
clustplotClass-class    clustplotClass class
convert_to_treedata     convert dataframe contained hierarchical
                        relationship or other classes to treedata class
data-hmp_aerobiosis_small
                        (Data) Small subset of the HMP 16S dataset
data-kostic2012crc      (Data) Genomic analysis identifies association
                        of Fusobacterium with colorectal carcinoma
                        (2012)
data-test_otu_data      (Data) simulated dataset.
diffAnalysisClass-class
                        diffAnalysisClass class
diff_analysis           Differential expression analysis
drop_taxa               Dropping Species with Few abundance and Few
                        Occurrences
generalizedFC           generalized fold change
get_alphaindex          alpha index
get_clust               Hierarchical cluster analysis for the samples
get_coord.pcoa          get ordination coordinates.
get_count               calculate the count or relative abundance of
                        replicate element with a speficify column
get_dist                calculate distance
get_mean_median         get the mean and median of specific feature.
get_pca                 Performs a principal components analysis
get_pcoa                performs principal coordinate analysis (PCoA)
get_pvalue              Methods for computation of the p-value
get_sampledflist        Generate random data list from a original data.
get_taxadf              get the data of specified taxonomy
get_upset               generate the dataset for upset of UpSetR
get_varct.pcoa          get the contribution of variables
get_vennlist            generate a vennlist for VennDiagram
ggbartax                taxonomy barplot
ggbox                   A box or violin plot with significance test
ggclust                 plot the result of hierarchical cluster
                        analysis for the samples
ggdiffbox               boxplot for the result of diff_analysis
ggdiffclade             plot the clade tree with highlight
ggdifftaxbar            significantly discriminative feature barplot
ggeffectsize            visualization of effect size by the Linear
                        Discriminant Analysis or randomForest
ggordpoint              ordination plotter based on ggplot2.
ggrarecurve             Rarefaction alpha index
import_dada2            Import function to load the feature table and
                        taxanomy table of dada2
import_qiime2           Import function to load the output of qiime2.
mapply_retrieve_seq     Retriveing Sequencing from NCBI By mapply
multi_compare           a container for performing two or more sample
                        test.
ordplotClass-class      ordplotClass class
pcasample-class         pcasample class
read_qza                read the qza file, output of qiime2.
retrieve_seq            Retriveing Sequencing from NCBI
show,diffAnalysisClass-method
                        method extensions to show for diffAnalysisClass
                        objects.
split_data              Split Large Vector or DataFrame
split_str_to_list       split a dataframe contained one column
theme_taxbar            theme_taxbar
