recipe bioconductor-meshes

MeSH Enrichment and Semantic analyses







biotools: meshes, doi: 10.1038/nmeth.3252

MeSH (Medical Subject Headings) is the NLM controlled vocabulary used to manually index articles for MEDLINE/PubMed. MeSH terms were associated by Entrez Gene ID by three methods, gendoo, gene2pubmed and RBBH. This association is fundamental for enrichment and semantic analyses. meshes supports enrichment analysis (over-representation and gene set enrichment analysis) of gene list or whole expression profile. The semantic comparisons of MeSH terms provide quantitative ways to compute similarities between genes and gene groups. meshes implemented five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively and supports more than 70 species.

package bioconductor-meshes

(downloads) docker_bioconductor-meshes



depends bioconductor-annotationdbi:


depends bioconductor-annotationhub:


depends bioconductor-dose:


depends bioconductor-enrichplot:


depends bioconductor-gosemsim:


depends bioconductor-meshdbi:


depends r-base:


depends r-yulab.utils:



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-meshes

and update with::

   mamba update bioconductor-meshes

To create a new environment, run:

mamba create --name myenvname bioconductor-meshes

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<tag>

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

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