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• W2070228064 abstract "RNA-seq, a massive parallel-sequencing-based transcriptome profiling method, provides digital data in the form of aligned sequence read counts. The comparative analyses of the data require appropriate statistical methods to estimate the differential expression of transcript variants across different cell/tissue types and disease conditions.We developed a novel nonparametric empirical Bayesian-based approach (NPEBseq) to model the RNA-seq data. The prior distribution of the Bayesian model is empirically estimated from the data without any parametric assumption, and hence the method is nonparametric in nature. Based on this model, we proposed a method for detecting differentially expressed genes across different conditions. We also extended this method to detect differential usage of exons from RNA-seq data. The evaluation of NPEBseq on both simulated and publicly available RNA-seq datasets and comparison with three popular methods showed improved results for experiments with or without biological replicates.NPEBseq can successfully detect differential expression between different conditions not only at gene level but also at exon level from RNA-seq datasets. In addition, NPEBSeq performs significantly better than current methods and can be applied to genome-wide RNA-seq datasets. Sample datasets and R package are available at http://bioinformatics.wistar.upenn.edu/NPEBseq." @default.
• W2070228064 created "2016-06-24" @default.
• W2070228064 creator A5017429478 @default.
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• W2070228064 date "2013-08-27" @default.
• W2070228064 modified "2023-10-07" @default.
• W2070228064 title "NPEBseq: nonparametric empirical bayesian-based procedure for differential expression analysis of RNA-seq data" @default.
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• W2070228064 doi "https://doi.org/10.1186/1471-2105-14-262" @default.
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