:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-perfect' .. highlight: bash bioconductor-perfect ==================== .. conda:recipe:: bioconductor-perfect :replaces_section_title: :noindex: Permutation filtration for microbiome data :homepage: https://bioconductor.org/packages/3.17/bioc/html/PERFect.html :license: Artistic-2.0 :recipe: /`bioconductor-perfect `_/`meta.yaml `_ PERFect is a novel permutation filtering approach designed to address two unsolved problems in microbiome data processing\: \(i\) define and quantify loss due to filtering by implementing thresholds\, and \(ii\) introduce and evaluate a permutation test for filtering loss to provide a measure of excessive filtering. .. conda:package:: bioconductor-perfect |downloads_bioconductor-perfect| |docker_bioconductor-perfect| :versions: ``1.14.0-0``,  ``1.12.0-0``,  ``1.8.0-0``,  ``1.6.0-0``,  ``1.4.0-1``,  ``1.4.0-0``,  ``1.2.0-0``,  ``1.0.0-0`` :depends bioconductor-phyloseq: ``>=1.44.0,<1.45.0`` :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-fitdistrplus: ``>=1.0.12`` :depends r-ggplot2: ``>=3.0.0`` :depends r-matrix: ``>=1.2.14`` :depends r-psych: ``>=1.8.4`` :depends r-sn: ``>=1.5.2`` :depends r-zoo: ``>=1.8.3`` :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-perfect and update with:: mamba update bioconductor-perfect To create a new environment, run:: mamba create --name myenvname bioconductor-perfect 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-perfect: (see `bioconductor-perfect/tags`_ for valid values for ````) .. |downloads_bioconductor-perfect| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-perfect.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-perfect :alt: (downloads) .. |docker_bioconductor-perfect| image:: https://quay.io/repository/biocontainers/bioconductor-perfect/status :target: https://quay.io/repository/biocontainers/bioconductor-perfect .. _`bioconductor-perfect/tags`: https://quay.io/repository/biocontainers/bioconductor-perfect?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-perfect/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-perfect/README.html