HMM-Fisher: identifying differential methylation using a hidden Markov model and Fisher's exact test

DOI10.1515/sagmb-2015-0076zbMath1343.92173OpenAlexW2411660950WikidataQ38795774 ScholiaQ38795774MaRDI QIDQ306662

Shuying Sun, Xiaoqing Yu

Publication date: 1 September 2016

Published in: Statistical Applications in Genetics and Molecular Biology (Search for Journal in Brave)

Full work available at URL: https://www.degruyter.com/view/j/sagmb.2016.15.issue-1/sagmb-2015-0076/sagmb-2015-0076.xml?format=INT

zbMATH Keywords

hidden Markov modelFisher's exact testbisulfite sequencingdifferential methylation

Mathematics Subject Classification ID

Computational methods in Markov chains (60J22) Biochemistry, molecular biology (92C40)

Related Items

HMM-DM: identifying differentially methylated regions using a hidden Markov model ⋮ Comparing five statistical methods of differential methylation identification using bisulfite sequencing data ⋮ A novel statistical method for modeling covariate effects in bisulfite sequencing derived measures of DNA methylation ⋮ HMM-Fisher

Uses Software

• Bioconductor
• SolexaQA
• Minfi
• methylKit
• BEAT
• BS Seeker
• TileQC
• BSmooth
• MethylSig
• Bisulfighter
• RRBSMAP
• HMM-DM
• DMAP
• MOABS
• SAAP-RRBS
• COHCAP
• IMA
• methyAnalysis
• MethylCoder

Cites Work

• HMM-DM: identifying differentially methylated regions using a hidden Markov model
• Comparing five statistical methods of differential methylation identification using bisulfite sequencing data
• Statistical Inference for Probabilistic Functions of Finite State Markov Chains