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

DOI10.1007/s13253-015-0232-3zbMath1329.62443OpenAlexW2279740950WikidataQ36827180 ScholiaQ36827180MaRDI QIDQ906080

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

zbMATH Keywords

geneticsempirical Bayessplit-plotintegrated nested Laplace approximationShrinkBayes

Mathematics Subject Classification ID

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

Related Items (1)

Fully Bayesian analysis of allele-specific RNA-seq data

Uses Software

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

Cites Work

• The importance of distinct modeling strategies for gene and gene-specific treatment effects in hierarchical models for microarray data
• DESeq2
• Statistical analysis of next generation sequencing data
• Fully Bayesian Mixture Model for Differential Gene Expression: Simulations and Model Checks
• Approximate Bayesian Inference for Latent Gaussian models by using Integrated Nested Laplace Approximations
• Multiple testing on standardized mortality ratios: a Bayesian hierarchical model for FDR estimation

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