recipe bioconductor-microbiomeprofiler

An R/shiny package for microbiome functional enrichment analysis

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/MicrobiomeProfiler.html

License:

GPL-2

Recipe:

/bioconductor-microbiomeprofiler/meta.yaml

This is an R/shiny package to perform functional enrichment analysis for microbiome data. This package was based on clusterProfiler. Moreover, MicrobiomeProfiler support KEGG enrichment analysis, COG enrichment analysis, Microbe-Disease association enrichment analysis, Metabo-Pathway analysis.

package bioconductor-microbiomeprofiler

versions:

1.8.0-0,  1.6.1-0,  1.4.0-0,  1.0.0-0

depends bioconductor-clusterprofiler:

>=4.10.0,<4.11.0

depends bioconductor-enrichplot:

>=1.22.0,<1.23.0

depends r-base:

>=4.3,<4.4.0a0

depends r-config:

depends r-dt:

depends r-ggplot2:

depends r-golem:

depends r-gson:

depends r-htmltools:

depends r-magrittr:

depends r-shiny:

>=1.6.0

depends r-shinycustomloader:

depends r-shinywidgets:

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-microbiomeprofiler

and update with::

   mamba update bioconductor-microbiomeprofiler

To create a new environment, run:

mamba create --name myenvname bioconductor-microbiomeprofiler

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-microbiomeprofiler:<tag>

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

Download stats

Link to this page

Render an 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-microbiomeprofiler/README.html)