recipe bioconductor-clusterprofiler

A universal enrichment tool for interpreting omics data

Homepage:

https://bioconductor.org/packages/3.17/bioc/html/clusterProfiler.html

License:

Artistic-2.0

Recipe:

/bioconductor-clusterprofiler/meta.yaml

Links:

biotools: clusterprofiler

This package supports functional characteristics of both coding and non-coding genomics data for thousands of species with up-to-date gene annotation. It provides a univeral interface for gene functional annotation from a variety of sources and thus can be applied in diverse scenarios. It provides a tidy interface to access, manipulate, and visualize enrichment results to help users achieve efficient data interpretation. Datasets obtained from multiple treatments and time points can be analyzed and compared in a single run, easily revealing functional consensus and differences among distinct conditions.

package bioconductor-clusterprofiler

versions:

4.8.1-0,  4.6.0-0,  4.2.0-0,  4.0.0-0,  3.18.1-0,  3.18.0-0,  3.16.0-0,  3.14.0-0,  3.12.0-1, 

4.8.1-0,  4.6.0-0,  4.2.0-0,  4.0.0-0,  3.18.1-0,  3.18.0-0,  3.16.0-0,  3.14.0-0,  3.12.0-1,  3.10.1-0,  3.8.1-0,  3.6.0-0,  3.4.4-0,  3.0.5-0,  3.0.4-1,  2.4.3-0

depends bioconductor-annotationdbi:

>=1.62.0,<1.63.0

depends bioconductor-dose:

>=3.26.0,<3.27.0

depends bioconductor-enrichplot:

>=1.20.0,<1.21.0

depends bioconductor-go.db:

>=3.17.0,<3.18.0

depends bioconductor-gosemsim:

>=2.26.0,<2.27.0

depends bioconductor-qvalue:

>=2.32.0,<2.33.0

depends r-base:

>=4.3,<4.4.0a0

depends r-downloader:

depends r-dplyr:

depends r-gson:

>=0.0.7

depends r-magrittr:

depends r-plyr:

depends r-rlang:

depends r-tidyr:

depends r-yulab.utils:

requirements:

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-clusterprofiler

and update with::

   mamba update bioconductor-clusterprofiler

To create a new environment, run:

mamba create --name myenvname bioconductor-clusterprofiler

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-clusterprofiler:<tag>

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

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