:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-meshes' .. highlight: bash bioconductor-meshes =================== .. conda:recipe:: bioconductor-meshes :replaces_section_title: :noindex: MeSH Enrichment and Semantic analyses :homepage: https://bioconductor.org/packages/3.18/bioc/html/meshes.html :license: Artistic-2.0 :recipe: /`bioconductor-meshes `_/`meta.yaml `_ :links: biotools: :biotools:`meshes`, doi: :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. .. conda:package:: bioconductor-meshes |downloads_bioconductor-meshes| |docker_bioconductor-meshes| :versions: .. raw:: html
1.28.0-01.26.0-01.24.0-01.20.0-01.18.0-01.16.0-11.16.0-01.14.0-01.12.0-0 ``1.28.0-0``,  ``1.26.0-0``,  ``1.24.0-0``,  ``1.20.0-0``,  ``1.18.0-0``,  ``1.16.0-1``,  ``1.16.0-0``,  ``1.14.0-0``,  ``1.12.0-0``,  ``1.10.0-1``,  ``1.8.0-0``,  ``1.6.1-0``,  ``1.4.0-0`` .. raw:: html
:depends bioconductor-annotationdbi: ``>=1.64.0,<1.65.0`` :depends bioconductor-annotationhub: ``>=3.10.0,<3.11.0`` :depends bioconductor-dose: ``>=3.28.0,<3.29.0`` :depends bioconductor-enrichplot: ``>=1.22.0,<1.23.0`` :depends bioconductor-gosemsim: ``>=2.28.0,<2.29.0`` :depends bioconductor-meshdbi: ``>=1.38.0,<1.39.0`` :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-yulab.utils: :requirements: .. rubric:: Installation You need a conda-compatible package manager (currently either `micromamba `_, `mamba `_, or `conda `_) and the Bioconda channel already activated (see :ref:`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 quay.io/biocontainers/bioconductor-meshes: (see `bioconductor-meshes/tags`_ for valid values for ````) .. |downloads_bioconductor-meshes| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-meshes.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-meshes :alt: (downloads) .. |docker_bioconductor-meshes| image:: https://quay.io/repository/biocontainers/bioconductor-meshes/status :target: https://quay.io/repository/biocontainers/bioconductor-meshes .. _`bioconductor-meshes/tags`: https://quay.io/repository/biocontainers/bioconductor-meshes?tab=tags .. raw:: html Download stats ----------------- .. raw:: html :file: ../../templates/package_dashboard.html Link to this page ----------------- Render an |install-with-bioconda| 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-meshes/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/bioconductor-meshes/README.html