recipe bioconductor-biomformat

An interface package for the BIOM file format







biotools: biomformat, doi: 10.1038/nmeth.3252

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.

package bioconductor-biomformat

(downloads) docker_bioconductor-biomformat



depends bioconductor-rhdf5:


depends r-base:


depends r-jsonlite:


depends r-matrix:


depends r-plyr:




You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-biomformat

and update with::

   mamba update bioconductor-biomformat

To create a new environment, run:

mamba create --name myenvname bioconductor-biomformat

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull<tag>

(see `bioconductor-biomformat/tags`_ for valid values for ``<tag>``)

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