Write, Analyze, and Visualize 'BIOM' Data

adiv_boxplot	Visualize alpha diversity with boxplots.
adiv_corrplot	Visualize alpha diversity with scatterplots and trendlines.
adiv_matrix	Create a matrix of samples x alpha diversity metrics.
adiv_stats	Test alpha diversity differences for significance.
adiv_table	Calculate the alpha diversity of each sample.
as.list.rbiom	Convert an rbiom object to a base R list.
as_rbiom	Convert a variety of data types to an rbiom object.
bdiv_boxplot	Visualize BIOM data with boxplots.
bdiv_corrplot	Visualize beta diversity with scatterplots and trendlines.
bdiv_heatmap	Display beta diversities in an all vs all grid.
bdiv_ord_plot	Ordinate samples and taxa on a 2D plane based on beta...
bdiv_ord_table	Calculate PCoA and other ordinations, including taxa biplots...
bdiv_stats	Test beta diversity vs categorical metadata.
bdiv_table	Distance / dissimilarity between samples.
bdply	Apply a function to each subset of an rbiom object.
biom_merge	Combine several rbiom objects into one.
convert_to_SE	Convert an rbiom object to a SummarizedExperiment object.
distmat_ord_table	Run ordinations on a distance matrix.
distmat_stats	Run statistics on a distance matrix vs a categorical or...
documentation_biom.rbiom	documentation_biom.rbiom
documentation_boxplot	documentation_boxplot
documentation_boxplot_aes_section	documentation_boxplot_aes_section
documentation_clusters	documentation_clusters
documentation_cmp	documentation_cmp
documentation_corrplot	documentation_corrplot
documentation_default	documentation_default
documentation_dist_test	documentation_dist_test
documentation_heatmap	documentation_heatmap
documentation_plot_return	documentation_plot_return
documentation_rank.NULL	documentation_rank.NULL
documentation_return.biom	documentation_return.biom
documentation_stats_return	documentation_stats_return
documentation_taxa.4	documentation_taxa.4
documentation_test.ifelse	documentation_test.ifelse
documentation_test.pw_means	documentation_test.pw_means
documentation_test.trends	documentation_test.trends
glimpse.rbiom	Get a glimpse of your metadata.
hmp50	Human Microbiome Project - 50 sample demo dataset.
mutate	Create, modify, and delete metadata fields.
plot_heatmap	Create a heatmap with tracks and dendrograms from any matrix.
pull.rbiom	Map sample names to metadata field values.
rare_corrplot	Visualize rarefaction curves with scatterplots and...
rarefy	Rarefy OTU counts.
rarefy_cols	Transform a counts matrix.
rare_multiplot	Combines rare_corrplot and rare_stacked into a single figure.
rare_stacked	Visualize the number of observations per sample.
rbiom-deprecated	Deprecated functions in package 'rbiom'.
rbiom_objects	Working with rbiom Objects.
rbiom-package	rbiom: Read/Write, Transform, and Summarize BIOM Data
read_fasta	Parse a fasta file into a named character vector.
read_tree	Read a newick formatted phylogenetic tree.
sample_sums	Sum the observations in each sample.
slice	Subset to a specific number of samples.
speed	Speed Ups.
subset	Subset an rbiom object by sample names or metadata.
taxa_boxplot	Visualize BIOM data with boxplots.
taxa_corrplot	Visualize taxa abundance with scatterplots and trendlines.
taxa_heatmap	Display taxa abundances as a heatmap.
taxa_map	Map OTUs names to taxa names at a given rank.
taxa_matrix	Taxa abundances per sample.
taxa_stacked	Display taxa abundances as a stacked bar graph.
taxa_stats	Test taxa abundances for significant differences.
taxa_sums	Get summary taxa abundances.
tree_subset	Create a subtree by specifying tips to keep.
write_biom	Save an rbiom object to a file.