Package Recipe 'bioconductor-methylumi'

recipe bioconductor-methylumi¶

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.

Homepage: https://bioconductor.org/packages/3.9/bioc/html/methylumi.html
License: GPL-2
Recipe: /bioconductor-methylumi/meta.yaml
Links: biotools: methylumi, doi: 10.1186/1471-2164-14-293

package bioconductor-methylumi¶

Versions: 2.28.0-0, 2.26.0-0, 2.24.1-0, 2.22.0-1, 2.22.0-0
Depends bioconductor-annotate: >=1.60.0,<1.61.0
Depends bioconductor-annotationdbi: >=1.44.0,<1.45.0
Depends bioconductor-biobase: >=2.42.0,<2.43.0
Depends bioconductor-biocgenerics: >=0.28.0,<0.29.0
Depends bioconductor-fdb.infiniummethylation.hg19: >=2.2.0,<2.3.0
Depends bioconductor-genefilter: >=1.64.0,<1.65.0
Depends bioconductor-genomeinfodb: >=1.18.0,<1.19.0
Depends bioconductor-genomicranges: >=1.34.0,<1.35.0
Depends bioconductor-illuminaio: >=0.24.0,<0.25.0
Depends bioconductor-iranges: >=2.16.0,<2.17.0
Depends bioconductor-minfi: >=1.28.0,<1.29.0
Depends bioconductor-s4vectors: >=0.20.0,<0.21.0
Depends bioconductor-summarizedexperiment: >=1.12.0,<1.13.0
Depends r-base: >=3.5.1,<3.5.2.0a0
Depends r-ggplot2
Depends r-lattice
Depends r-matrixstats
Depends r-reshape2
Depends r-scales
Requirements

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)