recipe bioconductor-comethdmr

Accurate identification of co-methylated and differentially methylated regions in epigenome-wide association studies

Homepage:

https://bioconductor.org/packages/3.16/bioc/html/coMethDMR.html

License:

GPL-3

Recipe:

/bioconductor-comethdmr/meta.yaml

coMethDMR identifies genomic regions associated with continuous phenotypes by optimally leverages covariations among CpGs within predefined genomic regions. Instead of testing all CpGs within a genomic region, coMethDMR carries out an additional step that selects co-methylated sub-regions first without using any outcome information. Next, coMethDMR tests association between methylation within the sub-region and continuous phenotype using a random coefficient mixed effects model, which models both variations between CpG sites within the region and differential methylation simultaneously.

package bioconductor-comethdmr

Versions:

1.2.0-0

Depends:

• bioconductor-annotationhub >=3.6.0,<3.7.0

• bioconductor-biocparallel >=1.32.0,<1.33.0

• bioconductor-bumphunter >=1.40.0,<1.41.0

• bioconductor-experimenthub >=2.6.0,<2.7.0

• bioconductor-genomicranges >=1.50.0,<1.51.0

• bioconductor-iranges >=2.32.0,<2.33.0

• r-base >=4.2,<4.3.0a0

• r-lmertest

Required By:

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-comethdmr

and update with:

conda update bioconductor-comethdmr

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-comethdmr:<tag>

(see bioconductor-comethdmr/tags for valid values for <tag>)

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