recipe bioconductor-methylumi

Handle Illumina methylation data

Homepage

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

License

GPL-2

Recipe

/bioconductor-methylumi/meta.yaml

Links

biotools: methylumi, doi: 10.1186/1471-2164-14-293

This package provides classes for holding and manipulating Illumina methylation data. Based on eSet, it can contain MIAME information, sample information, feature information, and multiple matrices of data. An "intelligent" import function, methylumiR can read the Illumina text files and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from HumanMethylation27 and HumanMethylation450 microarrays. Normalization, background correction, and quality control features for GoldenGate, Infinium, and Infinium HD arrays are also included.

package bioconductor-methylumi

Versions

2.34.0-0,  2.32.0-0,  2.30.0-1,  2.28.0-0,  2.26.0-0,  2.24.1-0,  2.22.0-1,  2.22.0-0

Depends

• bioconductor-annotate >=1.66.0,<1.67.0

• bioconductor-annotationdbi >=1.50.0,<1.51.0

• bioconductor-biobase >=2.48.0,<2.49.0

• bioconductor-biocgenerics >=0.34.0,<0.35.0

• bioconductor-fdb.infiniummethylation.hg19 >=2.2.0,<2.3.0

• bioconductor-genefilter >=1.70.0,<1.71.0

• bioconductor-genomeinfodb >=1.24.0,<1.25.0

• bioconductor-genomicranges >=1.40.0,<1.41.0

• bioconductor-illuminaio >=0.30.0,<0.31.0

• bioconductor-iranges >=2.22.0,<2.23.0

• bioconductor-minfi >=1.34.0,<1.35.0

• bioconductor-s4vectors >=0.26.0,<0.27.0

• bioconductor-summarizedexperiment >=1.18.0,<1.19.0

• r-base >=4.0,<4.1.0a0

• r-ggplot2

• r-lattice

• r-matrixstats

• r-reshape2

• r-scales

Required By

• bioconductor-skewr

• bioconductor-lumi

• bioconductor-missmethyl

• bioconductor-rnbeads

• bioconductor-bigmelon

• bioconductor-ffpe

• bioconductor-watermelon

• bioconductor-methyanalysis

Installation

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

conda install bioconductor-methylumi

and update with:

conda update bioconductor-methylumi

or use the docker container:

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

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

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-methylumi/README.html)