LuxHMM: DNA methylation analysis with genome segmentation via hidden Markov model.

ABSTRACT:

Background

DNA methylation plays an important role in studying the epigenetics of various biological processes including many diseases. Although differential methylation of individual cytosines can be informative, given that methylation of neighboring CpGs are typically correlated, analysis of differentially methylated regions is often of more interest.

Results

We have developed a probabilistic method and software, LuxHMM, that uses hidden Markov model (HMM) to segment the genome into regions and a Bayesian regression model, which allows handling of multiple covariates, to infer differential methylation of regions. Moreover, our model includes experimental parameters that describe the underlying biochemistry in bisulfite sequencing and model inference is done using either va

SUBMITTER: Malonzo MH 

PROVIDER: S-EPMC9945676 | biostudies-literature | 2023 Feb

REPOSITORIES: biostudies-literature