recipe bioconductor-gofuncr

Gene ontology enrichment using FUNC

Homepage:

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

License:

GPL (>= 2)

Recipe:

/bioconductor-gofuncr/meta.yaml

GOfuncR performs a gene ontology enrichment analysis based on the ontology enrichment software FUNC. GO-annotations are obtained from OrganismDb or OrgDb packages ('Homo.sapiens' by default); the GO-graph is included in the package and updated regularly (01-May-2021). GOfuncR provides the standard candidate vs. background enrichment analysis using the hypergeometric test, as well as three additional tests: (i) the Wilcoxon rank-sum test that is used when genes are ranked, (ii) a binomial test that is used when genes are associated with two counts and (iii) a Chi-square or Fisher's exact test that is used in cases when genes are associated with four counts. To correct for multiple testing and interdependency of the tests, family-wise error rates are computed based on random permutations of the gene-associated variables. GOfuncR also provides tools for exploring the ontology graph and the annotations, and options to take gene-length or spatial clustering of genes into account. It is also possible to provide custom gene coordinates, annotations and ontologies.

package bioconductor-gofuncr

versions:

1.20.0-0,  1.18.0-1,  1.18.0-0,  1.14.0-2,  1.14.0-1,  1.14.0-0,  1.12.0-0,  1.10.0-1,  1.10.0-0, 

1.20.0-0,  1.18.0-1,  1.18.0-0,  1.14.0-2,  1.14.0-1,  1.14.0-0,  1.12.0-0,  1.10.0-1,  1.10.0-0,  1.8.0-0,  1.6.0-0,  1.4.0-1,  1.2.0-0

depends bioconductor-annotationdbi:

>=1.62.0,<1.63.0

depends bioconductor-genomicranges:

>=1.52.0,<1.53.0

depends bioconductor-iranges:

>=2.34.0,<2.35.0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx-ng:

>=12

depends r-base:

>=4.3,<4.4.0a0

depends r-gtools:

>=3.5.0

depends r-mapplots:

>=1.5

depends r-rcpp:

>=0.11.5

depends r-vioplot:

>=0.2

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-gofuncr

and update with::

   mamba update bioconductor-gofuncr

To create a new environment, run:

mamba create --name myenvname bioconductor-gofuncr

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-gofuncr:<tag>

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

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