- recipe bioconductor-mira
Methylation-Based Inference of Regulatory Activity
DNA methylation contains information about the regulatory state of the cell. MIRA aggregates genome-scale DNA methylation data into a DNA methylation profile for a given region set with shared biological annotation. Using this profile, MIRA infers and scores the collective regulatory activity for the region set. MIRA facilitates regulatory analysis in situations where classical regulatory assays would be difficult and allows public sources of region sets to be leveraged for novel insight into the regulatory state of DNA methylation datasets.
- package bioconductor-mira¶
- depends bioconductor-biobase:
- depends bioconductor-biocgenerics:
- depends bioconductor-bsseq:
- depends bioconductor-genomicranges:
- depends bioconductor-iranges:
- depends bioconductor-s4vectors:
- depends r-base:
- depends r-data.table:
- depends r-ggplot2:
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-mira and update with:: mamba update bioconductor-mira
To create a new environment, run:
mamba create --name myenvname bioconductor-mira
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-mira:<tag> (see `bioconductor-mira/tags`_ for valid values for ``<tag>``)