:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-biomformat' .. highlight: bash bioconductor-biomformat ======================= .. conda:recipe:: bioconductor-biomformat :replaces_section_title: :noindex: An interface package for the BIOM file format :homepage: https://bioconductor.org/packages/3.18/bioc/html/biomformat.html :license: GPL-2 :recipe: /`bioconductor-biomformat `_/`meta.yaml `_ :links: biotools: :biotools:`biomformat`, doi: :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. .. conda:package:: bioconductor-biomformat |downloads_bioconductor-biomformat| |docker_bioconductor-biomformat| :versions: .. raw:: html
1.30.0-01.28.0-01.26.0-01.22.0-01.20.0-01.18.0-11.18.0-01.16.0-01.14.0-0 ``1.30.0-0``,  ``1.28.0-0``,  ``1.26.0-0``,  ``1.22.0-0``,  ``1.20.0-0``,  ``1.18.0-1``,  ``1.18.0-0``,  ``1.16.0-0``,  ``1.14.0-0``,  ``1.12.0-1``,  ``1.12.0-0``,  ``1.10.1-0``,  ``1.10.0-0``,  ``1.8.0-0``,  ``1.6.0-0``,  ``1.4.0-0``,  ``1.2.0-1``,  ``1.2.0-0``,  ``1.0.2-1``,  ``1.0.2-0`` .. raw:: html
:depends bioconductor-rhdf5: ``>=2.46.0,<2.47.0`` :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-jsonlite: ``>=0.9.16`` :depends r-matrix: ``>=1.2`` :depends r-plyr: ``>=1.8`` :requirements: .. rubric:: Installation You need a conda-compatible package manager (currently either `micromamba `_, `mamba `_, or `conda `_) and the Bioconda channel already activated (see :ref:`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 quay.io/biocontainers/bioconductor-biomformat: (see `bioconductor-biomformat/tags`_ for valid values for ````) .. |downloads_bioconductor-biomformat| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-biomformat.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-biomformat :alt: (downloads) .. |docker_bioconductor-biomformat| image:: https://quay.io/repository/biocontainers/bioconductor-biomformat/status :target: https://quay.io/repository/biocontainers/bioconductor-biomformat .. _`bioconductor-biomformat/tags`: https://quay.io/repository/biocontainers/bioconductor-biomformat?tab=tags .. raw:: html Download stats ----------------- .. raw:: html :file: ../../templates/package_dashboard.html Link to this page ----------------- Render an |install-with-bioconda| badge with the following MarkDown:: [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-biomformat/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/bioconductor-biomformat/README.html