recipe bioconductor-meal

Perform methylation analysis

Homepage:

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

License:

Artistic-2.0

Recipe:

/bioconductor-meal/meta.yaml

Package to integrate methylation and expression data. It can also perform methylation or expression analysis alone. Several plotting functionalities are included as well as a new region analysis based on redundancy analysis. Effect of SNPs on a region can also be estimated.

package bioconductor-meal

versions:

1.28.0-0,  1.22.0-0,  1.20.3-0,  1.20.0-0,  1.18.0-0,  1.15.0-0,  1.14.0-1,  1.12.0-0

depends bioconductor-biobase:

>=2.58.0,<2.59.0

depends bioconductor-biocgenerics:

>=0.44.0,<0.45.0

depends bioconductor-genomicranges:

>=1.50.0,<1.51.0

depends bioconductor-gviz:

>=1.42.0,<1.43.0

depends bioconductor-iranges:

>=2.32.0,<2.33.0

depends bioconductor-limma:

>=3.54.0,<3.55.0

depends bioconductor-minfi:

>=1.44.0,<1.45.0

depends bioconductor-missmethyl:

>=1.32.0,<1.33.0

depends bioconductor-multidataset:

>=1.26.0,<1.27.0

depends bioconductor-s4vectors:

>=0.36.0,<0.37.0

depends bioconductor-summarizedexperiment:

>=1.28.0,<1.29.0

depends r-base:

>=4.2,<4.3.0a0

depends r-ggplot2:

>=2.0.0

depends r-isva:

depends r-matrixstats:

depends r-permute:

depends r-smartsva:

depends r-vegan:

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-meal

and update with::

   mamba update bioconductor-meal

To create a new environment, run:

mamba create --name myenvname bioconductor-meal

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-meal:<tag>

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

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