All functions

format_phyloseq()

Formatting the phyloseq-class Object

format_to_besthit()

Formatting the phyloseq-class Object advanced

get_microbiome_data()

Download test microbiome data

list_microbiome_data()

List of available datasets

microbiome_pipeline()

Microbiome analysis pipeline

percent_classified()

Summarize the percent taxa classification for phyloseq-class

phy_to_ldf()

Convert phyloseq-class object to long data format

plot_alpha_diversities()

Creat a plot for alpha diversities calculated using the microbiome package

plot_ordiplot_core()

Plotting core microbiota on ordinations

plot_read_distribution()

Distribution of reads

plot_select_taxa()

A boxplot for user specified list of taxa

plot_taxa_boxplot()

Taxonomic Composition Plot boxplot

plot_taxa_composition()

Taxonomic Composition Plot

plot_taxa_cv()

Coefficient of variations

plot_taxa_heatmap()

Heatmap using phyloseq-class and pheatmap

print_ps()

Overview of phyloseq-class

taxa_summary()

Give taxa summary at specified taxonomic level

zackular2014

Test data