Empirical Bayes analysis of RNA-seq data for detection of gene expression heterosis

DOI10.1007/S13253-015-0230-5MaRDI QIDQ906083zbMATH OpenOpenAlexWikidataFDO

Authors Jarad Niemi, Eric Mittman, Will Landau, 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/pmc4852395

zbMATH Keywords

Bayesian Lassohierarchical modelhybrid vigornegative binomialparallel computingRNA-seq

Mathematics Subject Classification ID

Empirical decision procedures; empirical Bayes procedures (62C12) Bayesian inference (62F15) Applications of statistics to environmental and related topics (62P12)

Recommendations

• Estimation and testing of gene expression heterosis
• A semi-parametric Bayesian approach for differential expression analysis of RNA-seq data
• Hierarchical modeling and differential expression analysis for RNA-seq experiments with inbred and hybrid genotypes
• Detecting differential expression in RNA-sequence data using quasi-likelihood with shrunken dispersion estimates
• Empirical Bayes analysis of RNA sequencing experiments with auxiliary information

Cites work

• Approximate Bayesian inference for latent Gaussian models by using integrated nested Laplace approximations (with discussion)
• Bayesian lasso regression
• Estimation and testing of gene expression heterosis
• Inference from iterative simulation using multiple sequences
• MCMC using Hamiltonian dynamics
• Statistical analysis of next generation sequencing data
• The Bayesian Lasso

Cited in

(11)

• Bayesian analysis of RNA-Seq data using a family of negative binomial models
• Fully Bayesian analysis of allele-specific RNA-seq data
• An empirical Bayes testing procedure for detecting variants in analysis of next generation sequencing data
• Testing Sparsity-Inducing Penalties
• The NBP negative binomial model for assessing differential gene expression from RNA-Seq
• Estimation and testing of gene expression heterosis
• A semi-parametric Bayesian approach for detection of gene expression heterosis with RNA-seq data
• Detection of differentially expressed genes in discrete single‐cell RNA sequencing data using a hurdle model with correlated random effects
• Bayesian optimization sequential surrogate (BOSS) algorithm: fast Bayesian inference for a broad class of Bayesian hierarchical models
• A semi-parametric Bayesian approach for differential expression analysis of RNA-seq data
• Hierarchical modeling and differential expression analysis for RNA-seq experiments with inbred and hybrid genotypes

Describes a project that uses

Uses Software

• R
• Bioconductor
• edgeR
• doMC
• Stan
• BaySeq
• plyr
• RStan
• ShrinkBayes

This page was built for publication: Empirical Bayes analysis of RNA-seq data for detection of gene expression heterosis

Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q906083)