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Recently developed high-throughput sequencing technology named Methylated RNA Immunoprecipitation Sequencing (MeRIP-seq) enables one to profile mRNA epigenetic modification transcriptome wide. A few computational methods are available to identify transcriptome-wide mRNA modification, but they are either limited by over-simplified model ignoring the biological variance across replicates or suffer from low accuracy and efficiency.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>In this work, we develop a novel statistical method, based on an empirical Bayesian hierarchical model, to identify mRNA epigenetic modification regions from MeRIP-seq data. Our method accounts for various sources of variations in the data through rigorous modeling and applies shrinkage estimation by borrowing information from transcriptome-wide data to stabilize the parameter estimation. Simulation and real data analyses demonstrate that our method is more accurate, robust and efficient than the existing peak calling methods.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>Our method TRES is implemented as an R package and is freely available on Github at https:\/\/github.com\/ZhenxingGuo0015\/TRES.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab181","type":"journal-article","created":{"date-parts":[[2021,3,12]],"date-time":"2021-03-12T20:11:24Z","timestamp":1615579884000},"page":"2818-2824","source":"Crossref","is-referenced-by-count":18,"title":["Detecting m6A methylation regions from Methylated RNA Immunoprecipitation Sequencing"],"prefix":"10.1093","volume":"37","author":[{"given":"Zhenxing","family":"Guo","sequence":"first","affiliation":[{"name":"Department of Biostatistics and Bioinformatics, Emory University , Atlanta, GA 30322, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew M","family":"Shafik","sequence":"additional","affiliation":[{"name":"Department of Human Genetics, Emory University , Atlanta, GA 30322, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peng","family":"Jin","sequence":"additional","affiliation":[{"name":"Department of Human Genetics, Emory University , Atlanta, GA 30322, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhijin","family":"Wu","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, Brown University , Providence, RI 02806, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1269-7354","authenticated-orcid":false,"given":"Hao","family":"Wu","sequence":"additional","affiliation":[{"name":"Department of Biostatistics and Bioinformatics, Emory University , Atlanta, GA 30322, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2021,3,16]]},"reference":[{"key":"2023061310563703100_btab181-B1","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the false discovery rate: a practical and powerful approach to multiple testing","volume":"57","author":"Benjamini","year":"1995","journal-title":"J. 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