recipe bioconductor-mgnifyr

R interface to EBI MGnify metagenomics resource

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/MGnifyR.html

License:

Artistic-2.0 | file LICENSE

Recipe:

/bioconductor-mgnifyr/meta.yaml

Utility package to facilitate integration and analysis of EBI MGnify data in R. The package can be used to import microbial data for instance into TreeSummarizedExperiment (TreeSE). In TreeSE format, the data is directly compatible with miaverse framework.

package bioconductor-mgnifyr

versions:

1.2.0-0

depends bioconductor-biocgenerics:

>=0.52.0,<0.53.0

depends bioconductor-mia:

>=1.14.0,<1.15.0

depends bioconductor-multiassayexperiment:

>=1.32.0,<1.33.0

depends bioconductor-s4vectors:

>=0.44.0,<0.45.0

depends bioconductor-summarizedexperiment:

>=1.36.0,<1.37.0

depends bioconductor-treesummarizedexperiment:

>=2.14.0,<2.15.0

depends r-ape:

depends r-base:

>=4.4,<4.5.0a0

depends r-dplyr:

depends r-httr:

depends r-plyr:

depends r-reshape2:

depends r-tidyjson:

depends r-urltools:

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-mgnifyr

and update with::

   mamba update bioconductor-mgnifyr

To create a new environment, run:

mamba create --name myenvname bioconductor-mgnifyr

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-mgnifyr:<tag>

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

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