recipe bioconductor-orthogene

Interspecies gene mapping

Homepage:

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

License:

GPL-3

Recipe:

/bioconductor-orthogene/meta.yaml

`orthogene` is an R package for easy mapping of orthologous genes across hundreds of species. It pulls up-to-date gene ortholog mappings across **700+ organisms**. It also provides various utility functions to aggregate/expand common objects (e.g. data.frames, gene expression matrices, lists) using **1:1**, **many:1**, **1:many** or **many:many** gene mappings, both within- and between-species.

package bioconductor-orthogene

versions:

1.12.0-0,  1.8.0-0,  1.6.0-0,  1.4.0-0,  1.0.0-0

depends bioconductor-delayedarray:

>=0.32.0,<0.33.0

depends bioconductor-ggtree:

>=3.14.0,<3.15.0

depends r-babelgene:

depends r-base:

>=4.4,<4.5.0a0

depends r-data.table:

depends r-dplyr:

depends r-ggplot2:

depends r-ggpubr:

depends r-gprofiler2:

depends r-grr:

depends r-homologene:

depends r-jsonlite:

depends r-matrix:

depends r-patchwork:

depends r-repmis:

requirements:

additional platforms:

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-orthogene

and update with::

   mamba update bioconductor-orthogene

To create a new environment, run:

mamba create --name myenvname bioconductor-orthogene

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-orthogene:<tag>

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

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Link to this page

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