BNP-seq: Bayesian nonparametric differential expression analysis of sequencing count data
From MaRDI portal
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.
Recommendations
- The NBP negative binomial model for assessing differential gene expression from RNA-Seq
- A semi-parametric Bayesian approach for differential expression analysis of RNA-seq data
- Empirical likelihood tests for nonparametric detection of differential expression from RNA-seq data
- Bayesian analysis of RNA-Seq data using a family of negative binomial models
- Modeling overdispersion heterogeneity in differential expression analysis using mixtures
Cites work
- scientific article; zbMATH DE number 927302 (Why is no real title available?)
- scientific article; zbMATH DE number 227027 (Why is no real title available?)
- A Bayesian analysis of some nonparametric problems
- Bayesian nonparametric Plackett-Luce models for the analysis of preferences for college degree programmes
- Nonparametric Bayes estimators based on beta processes in models for life history data
- On Information and Sufficiency
- Statistical analysis of next generation sequencing data
Cited in
(18)- Empirical Bayes analysis of RNA sequencing experiments with auxiliary information
- Compressed spectral screening for large-scale differential correlation analysis with application in selecting glioblastoma gene modules
- Identifying atypically expressed chromosome regions using RNA-Seq data
- Fisher-Pitman Permutation Tests Based on Nonparametric Poisson Mixtures with Application to Single Cell Genomics
- Bayesian modeling of MPSS data: gene expression analysis of bovine \textit{salmonella} infection
- Shrinkage of dispersion parameters in the binomial family, with application to differential exon skipping
- Bayesian negative binomial mixture regression models for the analysis of sequence count and methylation data
- Empirical likelihood tests for nonparametric detection of differential expression from RNA-seq data
- The NBP negative binomial model for assessing differential gene expression from RNA-Seq
- A semi-parametric Bayesian approach for differential expression analysis of RNA-seq data
- Contrastive latent variable modeling with application to case-control sequencing experiments
- Modeling overdispersion heterogeneity in differential expression analysis using mixtures
- HmmSeq: a hidden Markov model for detecting differentially expressed genes from RNA-seq data
- Bayesian estimation of differential transcript usage from RNA-seq data
- Beta approximation of ratio distribution and its application to next generation sequencing read counts
- Bayesian analysis of RNA-Seq data using a family of negative binomial models
- Generate gene expression profile from high-throughput sequencing data
- A sparse negative binomial classifier with covariate adjustment for RNA-seq data
This page was built for publication: BNP-seq: Bayesian nonparametric differential expression analysis of sequencing count data
Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q4690929)
