All functions

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(<BIOM>)

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(<BIOM>)

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.