recipe bioconductor-seqgsea

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

Homepage

https://bioconductor.org/packages/3.11/bioc/html/SeqGSEA.html

License

GPL (>= 3)

Recipe

/bioconductor-seqgsea/meta.yaml

Links

biotools: seqgsea

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

1.28.0-0,  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 >=2.48.0,<2.49.0

• bioconductor-biomart >=2.44.0,<2.45.0

• bioconductor-deseq >=1.39.0,<1.40.0

• r-base >=4.0,<4.1.0a0

• r-doparallel

Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-seqgsea

and update with:

conda update bioconductor-seqgsea

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-seqgsea:<tag>

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

Link to this page

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