HMM-DM: identifying differentially methylated regions using a hidden Markov model
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Recommendations
- A hidden Markov model for identifying differentially methylated sites in bisulfite sequencing data
- A Bayesian hidden Markov model for detecting differentially methylated regions
- HMM-Fisher: identifying differential methylation using a hidden Markov model and Fisher's exact test
- Assessing genome-wide significance for the detection of differentially methylated regions
- An empirical Bayes approach for methylation differentiation at the single nucleotide resolution
Cites work
- Comparing five statistical methods of differential methylation identification using bisulfite sequencing data
- HMM-Fisher: identifying differential methylation using a hidden Markov model and Fisher's exact test
- methylKit
- Sampling-Based Approaches to Calculating Marginal Densities
- Slice sampling. (With discussions and rejoinder)
Cited in
(15)- Assessing genome-wide significance for the detection of differentially methylated regions
- MethCP: differentially methylated region detection with change point models
- Differential methylation tests of regulatory regions
- HMM-Fisher: identifying differential methylation using a hidden Markov model and Fisher's exact test
- Comparing five statistical methods of differential methylation identification using bisulfite sequencing data
- An empirical Bayes approach for methylation differentiation at the single nucleotide resolution
- Redefining CpG islands using hidden Markov models
- HMM-DM
- Incorporating genomic annotation into a hidden Markov model for DNA methylation tiling array data
- Integrating prior knowledge in multiple testing under dependence with applications to detecting differential DNA methylation
- Covariate adjusted differential variability analysis of DNA methylation with propensity score method
- A hidden Markov model for identifying differentially methylated sites in bisulfite sequencing data
- A Bayesian hidden Markov model for detecting differentially methylated regions
- A novel statistical method for modeling covariate effects in bisulfite sequencing derived measures of DNA methylation
- Nonparametric Bayes differential analysis of multigroup DNA methylation data
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