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.
With an activated Bioconda channel (see 2. Set up channels), install with:
conda install bioconductor-biomformat
and update with:
conda update bioconductor-biomformat
A Docker container is available at https://quay.io/repository/biocontainers/bioconductor-biomformat.