recipe bioconductor-missmethyl

Analysing Illumina HumanMethylation BeadChip Data

Homepage:

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

License:

GPL-2

Recipe:

/bioconductor-missmethyl/meta.yaml

Links:

biotools: missmethyl

Normalisation, testing for differential variability and differential methylation and gene set testing for data from Illumina's Infinium HumanMethylation arrays. The normalisation procedure is subset-quantile within-array normalisation (SWAN), which allows Infinium I and II type probes on a single array to be normalised together. The test for differential variability is based on an empirical Bayes version of Levene's test. Differential methylation testing is performed using RUV, which can adjust for systematic errors of unknown origin in high-dimensional data by using negative control probes. Gene ontology analysis is performed by taking into account the number of probes per gene on the array, as well as taking into account multi-gene associated probes.

package bioconductor-missmethyl

Versions:

1.32.0-0,  1.26.0-0,  1.24.0-1,  1.24.0-0,  1.22.0-0,  1.20.0-0,  1.18.0-1,  1.16.0-0,  1.14.0-0, 

1.32.0-0,  1.26.0-0,  1.24.0-1,  1.24.0-0,  1.22.0-0,  1.20.0-0,  1.18.0-1,  1.16.0-0,  1.14.0-0,  1.12.0-0

Depends:

• bioconductor-annotationdbi >=1.60.0,<1.61.0

• bioconductor-biobase >=2.58.0,<2.59.0

• bioconductor-biocgenerics >=0.44.0,<0.45.0

• bioconductor-genomicranges >=1.50.0,<1.51.0

• bioconductor-go.db >=3.16.0,<3.17.0

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

• bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0

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

• bioconductor-illuminahumanmethylationepicmanifest >=0.3.0,<0.4.0

• bioconductor-iranges >=2.32.0,<2.33.0

• bioconductor-limma >=3.54.0,<3.55.0

• bioconductor-methylumi >=2.44.0,<2.45.0

• bioconductor-minfi >=1.44.0,<1.45.0

• bioconductor-org.hs.eg.db >=3.16.0,<3.17.0

• bioconductor-s4vectors >=0.36.0,<0.37.0

• bioconductor-summarizedexperiment >=1.28.0,<1.29.0

• r-base >=4.2,<4.3.0a0

• r-biasedurn

• r-ruv

• r-statmod

• r-stringr

Required By:

• bioconductor-champ

• bioconductor-dmrcate

• bioconductor-methylgsa

• bioconductor-meal

Installation

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

conda install bioconductor-missmethyl

and update with:

conda update bioconductor-missmethyl

or use the docker container:

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

(see bioconductor-missmethyl/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-missmethyl/README.html)