recipe bioconductor-methylumi

Handle Illumina methylation data

Homepage:

https://bioconductor.org/packages/3.18/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:

2.48.0-0,  2.46.0-0,  2.44.0-0,  2.40.1-0,  2.38.0-0,  2.36.0-1,  2.36.0-0,  2.34.0-0,  2.32.0-0, 

2.48.0-0,  2.46.0-0,  2.44.0-0,  2.40.1-0,  2.38.0-0,  2.36.0-1,  2.36.0-0,  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:

>=1.80.0,<1.81.0

depends bioconductor-annotationdbi:

>=1.64.0,<1.65.0

depends bioconductor-biobase:

>=2.62.0,<2.63.0

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-fdb.infiniummethylation.hg19:

>=2.2.0,<2.3.0

depends bioconductor-genefilter:

>=1.84.0,<1.85.0

depends bioconductor-genomeinfodb:

>=1.38.0,<1.39.0

depends bioconductor-genomicfeatures:

>=1.54.0,<1.55.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-illuminaio:

>=0.44.0,<0.45.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends bioconductor-minfi:

>=1.48.0,<1.49.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends r-base:

>=4.3,<4.4.0a0

depends r-ggplot2:

depends r-lattice:

depends r-matrixstats:

depends r-reshape2:

depends r-scales:

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-methylumi

and update with::

   mamba update bioconductor-methylumi

To create a new environment, run:

mamba create --name myenvname bioconductor-methylumi

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

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

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

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