recipe bioconductor-recountmethylation

Access and analyze public DNA methylation array data compilations

Homepage:

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

License:

Artistic-2.0

Recipe:

/bioconductor-recountmethylation/meta.yaml

Resources for cross-study analyses of public DNAm array data from NCBI GEO repo, produced using Illumina's Infinium HumanMethylation450K (HM450K) and MethylationEPIC (EPIC) platforms. Provided functions enable download, summary, and filtering of large compilation files. Vignettes detail background about file formats, example analyses, and more. Note the disclaimer on package load and consult the main manuscripts for further info.

package bioconductor-recountmethylation

versions:

1.12.0-0,  1.10.0-0,  1.8.0-0,  1.4.0-0,  1.2.0-0,  1.0.0-2,  1.0.0-1

depends bioconductor-basilisk:

>=1.14.0,<1.15.0

depends bioconductor-biocfilecache:

>=2.10.0,<2.11.0

depends bioconductor-delayedmatrixstats:

>=1.24.0,<1.25.0

depends bioconductor-hdf5array:

>=1.30.0,<1.31.0

depends bioconductor-minfi:

>=1.48.0,<1.49.0

depends bioconductor-rhdf5:

>=2.46.0,<2.47.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends r-base:

>=4.3,<4.4.0a0

depends r-r.utils:

depends r-rcurl:

depends r-reticulate:

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-recountmethylation

and update with::

   mamba update bioconductor-recountmethylation

To create a new environment, run:

mamba create --name myenvname bioconductor-recountmethylation

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-recountmethylation:<tag>

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

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