All functions
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format_phyloseq()
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Formatting the phyloseq-class Object |
format_to_besthit()
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Formatting the phyloseq-class Object advanced |
get_microbiome_data()
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Download test microbiome data |
list_microbiome_data()
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List of available datasets |
microbiome_pipeline()
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Microbiome analysis pipeline |
percent_classified()
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Summarize the percent taxa classification for phyloseq-class |
phy_to_ldf()
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Convert phyloseq-class object to long data format |
plot_alpha_diversities()
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Creat a plot for alpha diversities calculated using the microbiome package |
plot_ordiplot_core()
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Plotting core microbiota on ordinations |
plot_read_distribution()
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Distribution of reads |
plot_select_taxa()
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A boxplot for user specified list of taxa |
plot_taxa_boxplot()
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Taxonomic Composition Plot boxplot |
plot_taxa_composition()
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Taxonomic Composition Plot |
plot_taxa_cv()
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Coefficient of variations |
plot_taxa_heatmap()
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Heatmap using phyloseq-class and pheatmap |
print_ps()
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Overview of phyloseq-class |
taxa_summary()
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Give taxa summary at specified taxonomic level |
zackular2014
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Test data |