recipe bioconductor-methylgsa

Gene Set Analysis Using the Outcome of Differential Methylation

Homepage

https://bioconductor.org/packages/3.14/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

1.10.0-0,  1.8.0-1,  1.8.0-0,  1.6.1-0,  1.4.0-0,  1.2.3-0,  1.0.2-0

Depends

• bioconductor-annotationdbi >=1.54.0,<1.55.0

• bioconductor-biocparallel >=1.26.0,<1.27.0

• bioconductor-clusterprofiler >=4.0.0,<4.1.0

• bioconductor-go.db >=3.13.0,<3.14.0

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

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

• bioconductor-missmethyl >=1.26.0,<1.27.0

• bioconductor-org.hs.eg.db >=3.13.0,<3.14.0

• bioconductor-reactome.db >=1.76.0,<1.77.0

• r-base >=4.1,<4.2.0a0

• 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>)

Download stats

Link to this page

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-methylgsa/README.html)