Detecting differential expression in RNA-sequence data using quasi-likelihood with shrunken dispersion estimates

DOI10.1515/1544-6115.1826zbMATH Open1296.92187OpenAlexW1490261451WikidataQ30574980 ScholiaQ30574980MaRDI QIDQ100304FDOQ100304

Gordon K. Smyth, Davis J. McCarthy, Steven P. Lund, Dan Nettleton

Publication date: 22 October 2012

Published in: Statistical Applications in Genetics and Molecular Biology (Search for Journal in Brave)

Full work available at URL: https://lib.dr.iastate.edu/cgi/viewcontent.cgi?article=1227&context=stat_las_pubs

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zbMATH Keywords

quasi-likelihooddifferential expressionRNA-seq

Mathematics Subject Classification ID

Protein sequences, DNA sequences (92D20)

Cited In (10)

• Detection of differentially expressed genes in discrete single‐cell RNA sequencing data using a hurdle model with correlated random effects
• What if we ignore the random effects when analyzing RNA-seq data in a multifactor experiment
• MSIQ: joint modeling of multiple RNA-seq samples for accurate isoform quantification
• Detecting rare and faint signals via thresholding maximum likelihood estimators
• QuasiSeq
• An Enhanced Quantile Approach for Assessing Differential Gene Expressions
• Modeling overdispersion heterogeneity in differential expression analysis using mixtures
• Detecting differentially expressed genes with RNA-seq data using backward selection to account for the effects of relevant covariates
• Estimation and testing of gene expression heterosis
• No counts, no variance: allowing for loss of degrees of freedom when assessing biological variability from RNA-seq data

Uses Software

• DEseq

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