BNP-seq: Bayesian nonparametric differential expression analysis of sequencing count data
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Abstract: We perform differential expression analysis of high-throughput sequencing count data under a Bayesian nonparametric framework, removing sophisticated ad-hoc pre-processing steps commonly required in existing algorithms. We propose to use the gamma (beta) negative binomial process, which takes into account different sequencing depths using sample-specific negative binomial probability (dispersion) parameters, to detect differentially expressed genes by comparing the posterior distributions of gene-specific negative binomial dispersion (probability) parameters. These model parameters are inferred by borrowing statistical strength across both the genes and samples. Extensive experiments on both simulated and real-world RNA sequencing count data show that the proposed differential expression analysis algorithms clearly outperform previously proposed ones in terms of the areas under both the receiver operating characteristic and precision-recall curves.
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Cited in
(18)- Bayesian analysis of RNA-Seq data using a family of negative binomial models
- Bayesian estimation of differential transcript usage from RNA-seq data
- Generate gene expression profile from high-throughput sequencing data
- A sparse negative binomial classifier with covariate adjustment for RNA-seq data
- Contrastive latent variable modeling with application to case-control sequencing experiments
- Identifying atypically expressed chromosome regions using RNA-Seq data
- Empirical Bayes analysis of RNA sequencing experiments with auxiliary information
- Modeling overdispersion heterogeneity in differential expression analysis using mixtures
- Shrinkage of dispersion parameters in the binomial family, with application to differential exon skipping
- The NBP negative binomial model for assessing differential gene expression from RNA-Seq
- Beta approximation of ratio distribution and its application to next generation sequencing read counts
- Bayesian negative binomial mixture regression models for the analysis of sequence count and methylation data
- Bayesian modeling of MPSS data: gene expression analysis of bovine \textit{salmonella} infection
- Empirical likelihood tests for nonparametric detection of differential expression from RNA-seq data
- Compressed spectral screening for large-scale differential correlation analysis with application in selecting glioblastoma gene modules
- Fisher-Pitman Permutation Tests Based on Nonparametric Poisson Mixtures with Application to Single Cell Genomics
- HmmSeq: a hidden Markov model for detecting differentially expressed genes from RNA-seq data
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