recipe bioconductor-pairedgsea

Paired DGE and DGS analysis for gene set enrichment analysis

Homepage:

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

License:

MIT + file LICENSE

Recipe:

/bioconductor-pairedgsea/meta.yaml

pairedGSEA makes it simple to run a paired Differential Gene Expression (DGE) and Differencital Gene Splicing (DGS) analysis. The package allows you to store intermediate results for further investiation, if desired. pairedGSEA comes with a wrapper function for running an Over-Representation Analysis (ORA) and functionalities for plotting the results.

package bioconductor-pairedgsea

versions:

1.2.0-0,  1.0.0-0

depends bioconductor-biocparallel:

>=1.36.0,<1.37.0

depends bioconductor-deseq2:

>=1.42.0,<1.43.0

depends bioconductor-dexseq:

>=1.48.0,<1.49.0

depends bioconductor-fgsea:

>=1.28.0,<1.29.0

depends bioconductor-limma:

>=3.58.0,<3.59.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends bioconductor-sva:

>=3.50.0,<3.51.0

depends r-aggregation:

depends r-base:

>=4.3,<4.4.0a0

depends r-ggplot2:

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-pairedgsea

and update with::

   mamba update bioconductor-pairedgsea

To create a new environment, run:

mamba create --name myenvname bioconductor-pairedgsea

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-pairedgsea:<tag>

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

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