recipe bioconductor-gosorensen

Statistical inference based on the Sorensen-Dice dissimilarity and the Gene Ontology (GO)

Homepage:

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

License:

GPL-3

Recipe:

/bioconductor-gosorensen/meta.yaml

This package implements inferential methods to compare gene lists in terms of their biological meaning as expressed in the GO. The compared gene lists are characterized by cross-tabulation frequency tables of enriched GO items. Dissimilarity between gene lists is evaluated using the Sorensen-Dice index. The fundamental guiding principle is that two gene lists are taken as similar if they share a great proportion of common enriched GO items.

package bioconductor-gosorensen

versions:

1.4.0-0,  1.2.0-0,  1.0.0-0

depends bioconductor-clusterprofiler:

>=4.10.0,<4.11.0

depends bioconductor-go.db:

>=3.18.0,<3.19.0

depends bioconductor-goprofiles:

>=1.64.0,<1.65.0

depends bioconductor-org.hs.eg.db:

>=3.18.0,<3.19.0

depends r-base:

>=4.3,<4.4.0a0

depends r-stringr:

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-gosorensen

and update with::

   mamba update bioconductor-gosorensen

To create a new environment, run:

mamba create --name myenvname bioconductor-gosorensen

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-gosorensen:<tag>

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

Download stats

Link to this page

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