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This is the development version of biomformat; for the stable release version, see biomformat.

An interface package for the BIOM file format

Bioconductor version: Development (3.20)

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 "4.4") and enter:

if (!require("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:

The biomformat package Vignette HTML R Script
Reference Manual PDF


biocViews DataImport, ImmunoOncology, Metagenomics, Microbiome, Software
Version 1.33.0
In Bioconductor since BioC 3.3 (R-3.3) (8 years)
License GPL-2
Depends R (>= 3.2), methods
Imports plyr (>= 1.8), jsonlite (>= 0.9.16), Matrix (>= 1.2), rhdf5
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Suggests testthat (>= 0.10), knitr (>= 1.10), BiocStyle(>= 1.6), rmarkdown (>= 0.7)
Linking To
Depends On Me
Imports Me microbiomeExplorer, microbiomeMarker, phyloseq
Suggests Me animalcules, metagenomeSeq, MGnifyR, mia, MicrobiotaProcess, MetaScope, metacoder
Links To Me
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Follow Installation instructions to use this package in your R session.

Source Package biomformat_1.33.0.tar.gz
Windows Binary
macOS Binary (x86_64) biomformat_1.33.0.tgz
macOS Binary (arm64) biomformat_1.33.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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