recipe bioconductor-seqgsea

Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing

Homepage:

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

License:

GPL (>= 3)

Recipe:

/bioconductor-seqgsea/meta.yaml

The package generally provides methods for gene set enrichment analysis of high-throughput RNA-Seq data by integrating differential expression and splicing. It uses negative binomial distribution to model read count data, which accounts for sequencing biases and biological variation. Based on permutation tests, statistical significance can also be achieved regarding each gene's differential expression and splicing, respectively.

package bioconductor-seqgsea

versions:

1.42.0-0,  1.40.0-0,  1.38.0-0,  1.34.0-0,  1.32.0-0,  1.28.0-0,  1.26.0-0,  1.24.0-1,  1.22.0-0, 

1.42.0-0,  1.40.0-0,  1.38.0-0,  1.34.0-0,  1.32.0-0,  1.28.0-0,  1.26.0-0,  1.24.0-1,  1.22.0-0,  1.20.0-0,  1.18.0-0,  1.16.0-0

depends bioconductor-biobase:

>=2.62.0,<2.63.0

depends bioconductor-biomart:

>=2.58.0,<2.59.0

depends bioconductor-deseq2:

>=1.42.0,<1.43.0

depends r-base:

>=4.3,<4.4.0a0

depends r-doparallel:

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-seqgsea

and update with::

   mamba update bioconductor-seqgsea

To create a new environment, run:

mamba create --name myenvname bioconductor-seqgsea

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-seqgsea:<tag>

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

Download stats

Link to this page

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