A package for identifying differentially methylated regions (DMRs) between case and control groups using whole genome bisulfite sequencing (WGBS) or reduced representative bisulfite sequencing (RRBS) experiment data.
The hummingbird package uses a Bayesian hidden Markov model (HMM) for detecting DMRs. It fits a Bayesian HMM for one chromosome at a time. The final output of hummingbird are the detected DMRs with start and end positions in a given chromosome, directions of the DMRs (hyper- or hypo-), and the numbers of CpGs in these DMRs.
The hummingbird package implements the algorithm described in the publication below.
The main functions of the package are: hummingbirdEM, hummingbirdPostAdjustment and hummingbirdGraph.
Eleni Adam, Tieming Ji, Desh Ranjan
Maintainer: Eleni Adam <email@example.com>
Ji (2019) A Bayesian hidden Markov model for detecting differentially methylated regions. Biometrics 75(2):663-673.
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