DOI: 10.18129/B9.bioc.biomformat    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see biomformat.

An interface package for the BIOM file format

Bioconductor version: 3.12

This is an R package for interfacing with the BIOM format. This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object (which is more complex than a single table), as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly "R flavor" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods.

Author: Paul J. McMurdie <mcmurdie at> and Joseph N Paulson <jpaulson at>

Maintainer: Paul J. McMurdie <mcmurdie at>

Citation (from within R, enter citation("biomformat")):


To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:



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biocViews DataImport, ImmunoOncology, Metagenomics, Microbiome, Software
Version 1.18.0
In Bioconductor since BioC 3.3 (R-3.3) (5 years)
License GPL-2
Depends R (>= 3.2), methods
Imports plyr (>= 1.8), jsonlite (>= 0.9.16), Matrix (>= 1.2), rhdf5
Suggests testthat (>= 0.10), knitr (>= 1.10), BiocStyle(>= 1.6), rmarkdown (>= 0.7)
Depends On Me
Imports Me animalcules, microbiomeExplorer, phyloseq
Suggests Me metagenomeSeq, MicrobiotaProcess
Links To Me
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Source Package biomformat_1.18.0.tar.gz
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