recipe bioconductor-dmrcate

Methylation array and sequencing spatial analysis methods

Homepage:

https://bioconductor.org/packages/3.17/bioc/html/DMRcate.html

License:

file LICENSE

Recipe:

/bioconductor-dmrcate/meta.yaml

Links:

biotools: dmrcate

De novo identification and extraction of differentially methylated regions (DMRs) from the human genome using Whole Genome Bisulfite Sequencing (WGBS) and Illumina Infinium Array (450K and EPIC) data. Provides functionality for filtering probes possibly confounded by SNPs and cross-hybridisation. Includes GRanges generation and plotting functions.

package bioconductor-dmrcate

versions:

2.12.0-0,  2.6.0-0,  2.4.1-0,  2.4.0-0,  2.2.0-0,  2.0.0-0,  1.20.0-1,  1.18.0-0,  1.16.0-0, 

2.12.0-0,  2.6.0-0,  2.4.1-0,  2.4.0-0,  2.2.0-0,  2.0.0-0,  1.20.0-1,  1.18.0-0,  1.16.0-0,  1.14.0-0

depends bioconductor-bsseq:

>=1.34.0,<1.35.0

depends bioconductor-dss:

>=2.46.0,<2.47.0

depends bioconductor-edger:

>=3.40.0,<3.41.0

depends bioconductor-experimenthub:

>=2.6.0,<2.7.0

depends bioconductor-genomeinfodb:

>=1.34.0,<1.35.0

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-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-plyr:

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-dmrcate

and update with::

   mamba update bioconductor-dmrcate

To create a new environment, run:

mamba create --name myenvname bioconductor-dmrcate

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-dmrcate:<tag>

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

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