recipe bioconductor-topgo

Enrichment Analysis for Gene Ontology

Homepage:

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

License:

LGPL

Recipe:

/bioconductor-topgo/meta.yaml

Links:

biotools: topgo, doi: 10.1093/bioinformatics/btl140

topGO package provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be implemented and applied.

package bioconductor-topgo

versions:

2.54.0-0,  2.52.0-0,  2.50.0-0,  2.46.0-0,  2.44.0-0,  2.42.0-1,  2.42.0-0,  2.41.0-0,  2.40.0-0, 

2.54.0-0,  2.52.0-0,  2.50.0-0,  2.46.0-0,  2.44.0-0,  2.42.0-1,  2.42.0-0,  2.41.0-0,  2.40.0-0,  2.37.0-0,  2.36.0-1,  2.34.0-0,  2.32.0-0,  2.30.0-0,  2.28.0-0,  2.24.0-1,  2.22.0-0

depends bioconductor-annotationdbi:

>=1.64.0,<1.65.0

depends bioconductor-biobase:

>=2.62.0,<2.63.0

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-go.db:

>=3.18.0,<3.19.0

depends bioconductor-graph:

>=1.80.0,<1.81.0

depends r-base:

>=4.3,<4.4.0a0

depends r-dbi:

depends r-lattice:

depends r-matrixstats:

depends r-sparsem:

>=0.73

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-topgo

and update with::

   mamba update bioconductor-topgo

To create a new environment, run:

mamba create --name myenvname bioconductor-topgo

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-topgo:<tag>

(see `bioconductor-topgo/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-topgo/README.html)