recipe bioconductor-magar

MAGAR: R-package to compute methylation Quantitative Trait Loci (methQTL) from DNA methylation and genotyping data

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/MAGAR.html

License:

GPL-3

Recipe:

/bioconductor-magar/meta.yaml

"Methylation-Aware Genotype Association in R" (MAGAR) computes methQTL from DNA methylation and genotyping data from matched samples. MAGAR uses a linear modeling stragety to call CpGs/SNPs that are methQTLs. MAGAR accounts for the local correlation structure of CpGs.

package bioconductor-magar

versions:

1.10.0-0,  1.8.0-0,  1.6.0-0,  1.2.0-0,  1.0.0-0

depends bioconductor-crlmm:

>=1.60.0,<1.61.0

depends bioconductor-hdf5array:

>=1.30.0,<1.31.0

depends bioconductor-impute:

>=1.76.0,<1.77.0

depends bioconductor-rnbeads:

>=2.20.0,<2.21.0

depends bioconductor-rnbeads.hg19:

>=1.34.0,<1.35.0

depends bioconductor-snpstats:

>=1.52.0,<1.53.0

depends r-argparse:

depends r-base:

>=4.3,<4.4.0a0

depends r-bigstatsr:

depends r-data.table:

depends r-doparallel:

depends r-ff:

depends r-igraph:

depends r-jsonlite:

depends r-plyr:

depends r-reshape2:

depends r-rjson:

depends r-upsetr:

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-magar

and update with::

   mamba update bioconductor-magar

To create a new environment, run:

mamba create --name myenvname bioconductor-magar

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-magar:<tag>

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

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