recipe bioconductor-methylgsa

Gene Set Analysis Using the Outcome of Differential Methylation

Homepage

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

License

GPL-2

Recipe

/bioconductor-methylgsa/meta.yaml

The main functions for methylGSA are methylglm and methylRRA. methylGSA implements logistic regression adjusting number of probes as a covariate. methylRRA adjusts multiple p-values of each gene by Robust Rank Aggregation. For more detailed help information, please see the vignette.

package bioconductor-methylgsa

Versions

1.6.1-0,  1.4.0-0,  1.2.3-0,  1.0.2-0

Depends

• bioconductor-annotationdbi >=1.50.0,<1.51.0

• bioconductor-biocparallel >=1.22.0,<1.23.0

• bioconductor-clusterprofiler >=3.16.0,<3.17.0

• bioconductor-go.db >=3.11.0,<3.12.0

• bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0

• bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19 >=0.6.0,<0.7.0

• bioconductor-missmethyl >=1.22.0,<1.23.0

• bioconductor-org.hs.eg.db >=3.11.0,<3.12.0

• bioconductor-reactome.db >=1.70.0,<1.71.0

• r-base >=4.0,<4.1.0a0

• r-ggplot2

• r-robustrankaggreg

• r-shiny

• r-stringr

Required By

Installation

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

conda install bioconductor-methylgsa

and update with:

conda update bioconductor-methylgsa

or use the docker container:

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

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

Link to this page

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