recipe bioconductor-mosdef

MOSt frequently used and useful Differential Expression Functions

Homepage:

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

License:

MIT + file LICENSE

Recipe:

/bioconductor-mosdef/meta.yaml

This package provides functionality to run a number of tasks in the differential expression analysis workflow. This encompasses the most widely used steps, from running various enrichment analysis tools with a unified interface to creating plots and beautifying table components linking to external websites and databases. This streamlines the generation of comprehensive analysis reports.

package bioconductor-mosdef

versions:

1.2.0-0

depends bioconductor-annotationdbi:

>=1.68.0,<1.69.0

depends bioconductor-clusterprofiler:

>=4.14.0,<4.15.0

depends bioconductor-deseq2:

>=1.46.0,<1.47.0

depends bioconductor-go.db:

>=3.20.0,<3.21.0

depends bioconductor-goseq:

>=1.58.0,<1.59.0

depends bioconductor-s4vectors:

>=0.44.0,<0.45.0

depends bioconductor-summarizedexperiment:

>=1.36.0,<1.37.0

depends bioconductor-topgo:

>=2.58.0,<2.59.0

depends r-base:

>=4.4,<4.5.0a0

depends r-dt:

depends r-ggforce:

depends r-ggplot2:

depends r-ggrepel:

depends r-htmltools:

depends r-rcolorbrewer:

depends r-rlang:

depends r-scales:

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-mosdef

and update with::

   mamba update bioconductor-mosdef

To create a new environment, run:

mamba create --name myenvname bioconductor-mosdef

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-mosdef:<tag>

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

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Link to this page

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