:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'maaslin2' .. highlight: bash maaslin2 ======== .. conda:recipe:: maaslin2 :replaces_section_title: :noindex: MaAsLin2 is comprehensive R package for efficiently determining multivariable association between microbial meta\'omic features and clinical metadata. :homepage: http://huttenhower.sph.harvard.edu/maaslin2 :license: Custom OSS :recipe: /`maaslin2 `_/`meta.yaml `_ .. conda:package:: maaslin2 |downloads_maaslin2| |docker_maaslin2| :versions: ``0.99.12-0``,  ``0.99.2-0``,  ``0.99.1-0``,  ``0.3.0-0`` :depends bioconductor-edger: :depends bioconductor-metagenomeseq: :depends r-base: ``>=3.6,<3.7.0a0`` :depends r-car: :depends r-chemometrics: :depends r-cplm: :depends r-data.table: :depends r-dplyr: :depends r-ggplot2: :depends r-hash: :depends r-lmertest: :depends r-logging: :depends r-mass: :depends r-mumin: :depends r-optparse: :depends r-pbapply: :depends r-pheatmap: :depends r-pscl: :depends r-vegan: :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 maaslin2 and update with:: mamba update maaslin2 To create a new environment, run:: mamba create --name myenvname maaslin2 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/maaslin2: (see `maaslin2/tags`_ for valid values for ````) .. |downloads_maaslin2| image:: https://img.shields.io/conda/dn/bioconda/maaslin2.svg?style=flat :target: https://anaconda.org/bioconda/maaslin2 :alt: (downloads) .. |docker_maaslin2| image:: https://quay.io/repository/biocontainers/maaslin2/status :target: https://quay.io/repository/biocontainers/maaslin2 .. _`maaslin2/tags`: https://quay.io/repository/biocontainers/maaslin2?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/maaslin2/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/maaslin2/README.html