recipe bioconductor-phosr

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.

package 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:

additional platforms:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see 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:<tag>

(see `bioconductor-phosr/tags`_ for valid values for ``<tag>``)

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Link to this page

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