microbiomeutilities: An R package for utilities to guide in-depth marker gene amplicon data analysis


[Up] [Top]

Documentation for package ‘microbiomeutilities’ version 0.99.02

Help Pages

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_ordination_utils Plot species loading with ordinations
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