MIRA (Methylation-based Inference of Regulatory Activity)
The MIRA package aggregates DNA methylation across the genome for instances of a genomic feature like histone ChIP peaks, transcription factor ChIP peaks, or open chromatin regions in order to give a single signature and score for that feature, which may be used to infer regulatory activity.
MIRA may be installed from Github:
or locally after downloading/cloning the source code:
install.packages("path/to/MIRA/directory", repos=NULL, type="source")
Learning how to use MIRA
A couple of vignettes are included with the package. For an overview of the package see the "Getting Started" vignette. A more realistic example of how to use MIRA may be found in the "BiologicalApplication" vignette.