DOI: 10.18129/B9.bioc.biomformat    

This is the development version of biomformat; to use it, please install the devel version of Bioconductor.

An interface package for the BIOM file format

Bioconductor version: Development (3.10)

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 "3.6") and enter:

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

# The following initializes usage of Bioc devel


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:



HTML R Script The biomformat package Vignette
PDF   Reference Manual
Text   NEWS


biocViews DataImport, ImmunoOncology, Metagenomics, Microbiome, Software
Version 1.13.0
In Bioconductor since BioC 3.3 (R-3.3) (3 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 phyloseq
Suggests Me metagenomeSeq
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package biomformat_1.13.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) biomformat_1.13.0.tgz
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