recipe bioconductor-methylmix

MethylMix: Identifying methylation driven cancer genes

Homepage:

https://bioconductor.org/packages/3.16/bioc/html/MethylMix.html

License:

GPL-2

Recipe:

/bioconductor-methylmix/meta.yaml

MethylMix is an algorithm implemented to identify hyper and hypomethylated genes for a disease. MethylMix is based on a beta mixture model to identify methylation states and compares them with the normal DNA methylation state. MethylMix uses a novel statistic, the Differential Methylation value or DM-value defined as the difference of a methylation state with the normal methylation state. Finally, matched gene expression data is used to identify, besides differential, functional methylation states by focusing on methylation changes that effect gene expression. References: Gevaert 0. MethylMix: an R package for identifying DNA methylation-driven genes. Bioinformatics (Oxford, England). 2015;31(11):1839-41. doi:10.1093/bioinformatics/btv020. Gevaert O, Tibshirani R, Plevritis SK. Pancancer analysis of DNA methylation-driven genes using MethylMix. Genome Biology. 2015;16(1):17. doi:10.1186/s13059-014-0579-8.

package bioconductor-methylmix

Versions:

2.28.0-0,  2.24.0-0,  2.22.0-0,  2.20.0-1,  2.20.0-0,  2.18.0-0,  2.16.0-0,  2.14.0-1,  2.14.0-0, 

2.28.0-0,  2.24.0-0,  2.22.0-0,  2.20.0-1,  2.20.0-0,  2.18.0-0,  2.16.0-0,  2.14.0-1,  2.14.0-0,  2.12.0-0

Depends:

• bioconductor-impute >=1.72.0,<1.73.0

• bioconductor-limma >=3.54.0,<3.55.0

• r-base >=4.2,<4.3.0a0

• r-data.table

• r-digest

• r-foreach

• r-ggplot2

• r-r.matlab

• r-rcolorbrewer

• r-rcurl

• r-rpmm

Required By:

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-methylmix

and update with:

conda update bioconductor-methylmix

or use the docker container:

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

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

Download stats

Link to this page

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