- recipe bioconductor-comethdmr
Accurate identification of co-methylated and differentially methylated regions in epigenome-wide association studies
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¶
- depends bioconductor-annotationhub:
- depends bioconductor-biocparallel:
- depends bioconductor-bumphunter:
- depends bioconductor-experimenthub:
- depends bioconductor-genomicranges:
- depends bioconductor-iranges:
- depends r-base:
- depends r-lmertest:
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-comethdmr and update with:: mamba update bioconductor-comethdmr
To create a new environment, run:
mamba create --name myenvname bioconductor-comethdmr
myenvnamebeing 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-comethdmr:<tag> (see `bioconductor-comethdmr/tags`_ for valid values for ``<tag>``)