recipe bioconductor-dose

Disease Ontology Semantic and Enrichment analysis

Homepage:

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

License:

Artistic-2.0

Recipe:

/bioconductor-dose/meta.yaml

Links:

biotools: dose

This package implements five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively for measuring semantic similarities among DO terms and gene products. Enrichment analyses including hypergeometric model and gene set enrichment analysis are also implemented for discovering disease associations of high-throughput biological data.

package bioconductor-dose

versions:

3.28.1-0,  3.26.1-0,  3.24.0-0,  3.20.0-0,  3.18.0-0,  3.16.0-1,  3.16.0-0,  3.14.0-0,  3.12.0-0, 

3.28.1-0,  3.26.1-0,  3.24.0-0,  3.20.0-0,  3.18.0-0,  3.16.0-1,  3.16.0-0,  3.14.0-0,  3.12.0-0,  3.10.2-0,  3.8.0-0,  3.6.1-0,  3.4.0-0,  3.2.0-0,  2.10.7-0,  2.10.6-0,  2.8.3-0,  2.8.2-0

depends bioconductor-annotationdbi:

>=1.64.0,<1.65.0

depends bioconductor-biocparallel:

>=1.36.0,<1.37.0

depends bioconductor-fgsea:

>=1.28.0,<1.29.0

depends bioconductor-gosemsim:

>=2.28.0,<2.29.0

depends bioconductor-hdo.db:

>=0.99.0,<0.100.0

depends bioconductor-qvalue:

>=2.34.0,<2.35.0

depends r-base:

>=4.3,<4.4.0a0

depends r-ggplot2:

depends r-reshape2:

depends r-yulab.utils:

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-dose

and update with::

   mamba update bioconductor-dose

To create a new environment, run:

mamba create --name myenvname bioconductor-dose

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-dose:<tag>

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

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