alpha.div               Estimate the diversity of each sample.
beta.div                Make a distance matrix of samples vs samples.
counts                  Get the abundance counts.
info                    Get biom's misc information.
metadata                Get the sample metadata.
nsamples                Number of samples in a BIOM.
ntaxa                   Number of taxa in a BIOM.
phylogeny               Get the phylogenetic tree.
print                   Summarize the contents of a BIOM object
rarefy                  Subset counts so that all samples have the same
                        number of observations.
rbiom                   rbiom: Read/Write, Transform, and Summarize
                        BIOM Data
read.biom               Extracts counts, metadata, taxonomy, and
                        phylogeny from a biom file.
read.fasta              Parse a fasta file into a named character
                        vector.
read.tree               Read a newick formatted phylogenetic tree.
sample.names            Get the sample names.
select                  Reduce samples to a specific list
sequences               DNA sequence associated with each taxonomic
                        identifier.
subset                  Subset samples using the BIOM object's metadata
subtree                 Create a subtree by specifying tips to keep.
taxa.names              Get the taxa names.
taxa.ranks              Get the taxa ranks.
taxa.rollup             Generate a matrix of samples by taxa, at the
                        specified taxonomic rank.
taxonomy                Get the taxonomy table.
tips                    Names of a phylogenetic tree's tips/leafs.
unifrac                 Compute Weighted and Unweighted UniFrac
                        distance matrices.
write.biom              Write counts, metadata, taxonomy, and phylogeny
                        to a biom file.
write.fasta             Write sequences from a BIOM object to a file in
                        fasta format.
write.tree              Write a newick formatted phylogenetic tree.
write.xlsx              Write data and summary information to a
                        Microsoft Excel-compatible workbook.
