:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-phyloseq' .. highlight: bash bioconductor-phyloseq ===================== .. conda:recipe:: bioconductor-phyloseq :replaces_section_title: :noindex: Handling and analysis of high\-throughput microbiome census data :homepage: https://bioconductor.org/packages/3.18/bioc/html/phyloseq.html :license: AGPL-3 :recipe: /`bioconductor-phyloseq `_/`meta.yaml `_ :links: biotools: :biotools:`phyloseq` phyloseq provides a set of classes and tools to facilitate the import\, storage\, analysis\, and graphical display of microbiome census data. .. conda:package:: bioconductor-phyloseq |downloads_bioconductor-phyloseq| |docker_bioconductor-phyloseq| :versions: .. raw:: html
1.46.0-01.44.0-01.42.0-01.38.0-01.36.0-01.34.0-11.34.0-01.32.0-01.30.0-0 ``1.46.0-0``,  ``1.44.0-0``,  ``1.42.0-0``,  ``1.38.0-0``,  ``1.36.0-0``,  ``1.34.0-1``,  ``1.34.0-0``,  ``1.32.0-0``,  ``1.30.0-0``,  ``1.28.0-1``,  ``1.26.1-0``,  ``1.26.0-0``,  ``1.24.2-0``,  ``1.22.3-0``,  ``1.20.0-1``,  ``1.20.0-0``,  ``1.19.1-0``,  ``1.16.2-1``,  ``1.14.0-0`` .. raw:: html
:depends bioconductor-biobase: ``>=2.62.0,<2.63.0`` :depends bioconductor-biocgenerics: ``>=0.48.0,<0.49.0`` :depends bioconductor-biomformat: ``>=1.30.0,<1.31.0`` :depends bioconductor-biostrings: ``>=2.70.0,<2.71.0`` :depends bioconductor-multtest: ``>=2.58.0,<2.59.0`` :depends r-ade4: ``>=1.7-4`` :depends r-ape: ``>=5.0`` :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-cluster: ``>=2.0.4`` :depends r-data.table: ``>=1.10.4`` :depends r-foreach: ``>=1.4.3`` :depends r-ggplot2: ``>=2.1.0`` :depends r-igraph: ``>=1.0.1`` :depends r-plyr: ``>=1.8.3`` :depends r-reshape2: ``>=1.4.1`` :depends r-scales: ``>=0.4.0`` :depends r-vegan: ``>=2.5`` :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-phyloseq and update with:: mamba update bioconductor-phyloseq To create a new environment, run:: mamba create --name myenvname bioconductor-phyloseq 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-phyloseq: (see `bioconductor-phyloseq/tags`_ for valid values for ````) .. |downloads_bioconductor-phyloseq| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-phyloseq.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-phyloseq :alt: (downloads) .. |docker_bioconductor-phyloseq| image:: https://quay.io/repository/biocontainers/bioconductor-phyloseq/status :target: https://quay.io/repository/biocontainers/bioconductor-phyloseq .. _`bioconductor-phyloseq/tags`: https://quay.io/repository/biocontainers/bioconductor-phyloseq?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-phyloseq/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-phyloseq/README.html