:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-magar' .. highlight: bash bioconductor-magar ================== .. conda:recipe:: bioconductor-magar :replaces_section_title: :noindex: 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. .. conda:package:: bioconductor-magar |downloads_bioconductor-magar| |docker_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: .. rubric:: Installation You need a conda-compatible package manager (currently either `micromamba `_, `mamba `_, or `conda `_) and the Bioconda channel already activated (see :ref:`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: (see `bioconductor-magar/tags`_ for valid values for ````) .. |downloads_bioconductor-magar| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-magar.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-magar :alt: (downloads) .. |docker_bioconductor-magar| image:: https://quay.io/repository/biocontainers/bioconductor-magar/status :target: https://quay.io/repository/biocontainers/bioconductor-magar .. _`bioconductor-magar/tags`: https://quay.io/repository/biocontainers/bioconductor-magar?tab=tags .. raw:: html Download stats ----------------- .. raw:: html :file: ../../templates/package_dashboard.html Link to this page ----------------- Render an |install-with-bioconda| 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-magar/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/bioconductor-magar/README.html