recipe bioconductor-mcsea

Methylated CpGs Set Enrichment Analysis

Homepage:

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

License:

GPL-2

Recipe:

/bioconductor-mcsea/meta.yaml

Identification of diferentially methylated regions (DMRs) in predefined regions (promoters, CpG islands…) from the human genome using Illumina's 450K or EPIC microarray data. Provides methods to rank CpG probes based on linear models and includes plotting functions.

package bioconductor-mcsea

versions:

1.22.0-0,  1.20.0-0,  1.18.0-0,  1.14.0-0,  1.12.0-0,  1.10.0-2,  1.10.0-0,  1.8.0-0,  1.6.0-1, 

1.22.0-0,  1.20.0-0,  1.18.0-0,  1.14.0-0,  1.12.0-0,  1.10.0-2,  1.10.0-0,  1.8.0-0,  1.6.0-1,  1.4.0-1,  1.2.0-0

depends bioconductor-biomart:

>=2.58.0,<2.59.0

depends bioconductor-fgsea:

>=1.28.0,<1.29.0

depends bioconductor-genomicfeatures:

>=1.54.0,<1.55.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-gviz:

>=1.46.0,<1.47.0

depends bioconductor-homo.sapiens:

>=1.3.0,<1.4.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends bioconductor-limma:

>=3.58.0,<3.59.0

depends bioconductor-mcseadata:

>=1.22.0,<1.23.0

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:

requirements:

additional platforms:

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-mcsea

and update with::

   mamba update bioconductor-mcsea

To create a new environment, run:

mamba create --name myenvname bioconductor-mcsea

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-mcsea:<tag>

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

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