Hierarchical modeling and differential expression analysis for RNA-seq experiments with inbred and hybrid genotypes

DOI10.1007/S13253-015-0232-3zbMATH Open1329.62443OpenAlexW2279740950WikidataQ36827180 ScholiaQ36827180MaRDI QIDQ906080FDOQ906080

Andrew Lithio, Dan Nettleton

Publication date: 29 January 2016

Published in: Journal of Agricultural, Biological and Environmental Statistics (Search for Journal in Brave)

Full work available at URL: http://europepmc.org/articles/pmc4841633

Recommendations

• Empirical Bayes analysis of RNA-seq data for detection of gene expression heterosis
• A semi-parametric Bayesian approach for differential expression analysis of RNA-seq data
• Detecting differential expression in RNA-sequence data using quasi-likelihood with shrunken dispersion estimates
• Detecting differentially expressed genes with RNA-seq data using backward selection to account for the effects of relevant covariates
• Contrastive latent variable modeling with application to case-control sequencing experiments

zbMATH Keywords

geneticsempirical Bayessplit-plotintegrated nested Laplace approximationShrinkBayes

Mathematics Subject Classification ID

Bayesian inference (62F15) Generalized linear models (logistic models) (62J12) Applications of statistics to environmental and related topics (62P12) Protein sequences, DNA sequences (92D20) Empirical decision procedures; empirical Bayes procedures (62C12)

Cites Work

• Approximate Bayesian inference for latent Gaussian models by using integrated nested Laplace approximations (with discussion)
• DESeq2
• The importance of distinct modeling strategies for gene and gene-specific treatment effects in hierarchical models for microarray data
• Statistical analysis of next generation sequencing data
• Fully Bayesian mixture model for differential gene expression: simulations and model checks
• Multiple testing on standardized mortality ratios: a Bayesian hierarchical model for FDR estimation

Cited In (1)

• Fully Bayesian analysis of allele-specific RNA-seq data

Uses Software

• Bioconductor
• gcrma
• edgeR
• BaySeq
• DEseq
• limma
• ShrinkBayes
• Voom
• DESeq2

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