:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-phosr' .. highlight: bash bioconductor-phosr ================== .. conda:recipe:: bioconductor-phosr :replaces_section_title: :noindex: A set of methods and tools for comprehensive analysis of phosphoproteomics data :homepage: https://bioconductor.org/packages/3.18/bioc/html/PhosR.html :license: GPL-3 + file LICENSE :recipe: /`bioconductor-phosr `_/`meta.yaml `_ PhosR is a package for the comprenhensive analysis of phosphoproteomic data. There are two major components to PhosR\: processing and downstream analysis. PhosR consists of various processing tools for phosphoproteomics data including filtering\, imputation\, normalisation\, and functional analysis for inferring active kinases and signalling pathways. .. conda:package:: bioconductor-phosr |downloads_bioconductor-phosr| |docker_bioconductor-phosr| :versions: ``1.12.0-0``,  ``1.10.0-0``,  ``1.8.0-0``,  ``1.4.0-0``,  ``1.2.0-0``,  ``1.0.0-2``,  ``1.0.0-1`` :depends bioconductor-biocgenerics: ``>=0.48.0,<0.49.0`` :depends bioconductor-limma: ``>=3.58.0,<3.59.0`` :depends bioconductor-pcamethods: ``>=1.94.0,<1.95.0`` :depends bioconductor-preprocesscore: ``>=1.64.0,<1.65.0`` :depends bioconductor-s4vectors: ``>=0.40.0,<0.41.0`` :depends bioconductor-summarizedexperiment: ``>=1.32.0,<1.33.0`` :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-circlize: :depends r-dendextend: :depends r-dplyr: :depends r-e1071: :depends r-ggally: :depends r-ggdendro: :depends r-ggplot2: :depends r-ggpubr: :depends r-ggtext: :depends r-igraph: :depends r-network: :depends r-pheatmap: :depends r-rcolorbrewer: :depends r-reshape2: :depends r-rlang: :depends r-ruv: :depends r-stringi: :depends r-tidyr: :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-phosr and update with:: mamba update bioconductor-phosr To create a new environment, run:: mamba create --name myenvname bioconductor-phosr 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-phosr: (see `bioconductor-phosr/tags`_ for valid values for ````) .. |downloads_bioconductor-phosr| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-phosr.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-phosr :alt: (downloads) .. |docker_bioconductor-phosr| image:: https://quay.io/repository/biocontainers/bioconductor-phosr/status :target: https://quay.io/repository/biocontainers/bioconductor-phosr .. _`bioconductor-phosr/tags`: https://quay.io/repository/biocontainers/bioconductor-phosr?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-phosr/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-phosr/README.html