What if we ignore the random effects when analyzing RNA-seq data in a multifactor experiment

EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments

(2013) Ning Leng et al.   BIOINFORMATICS

Empirical Bayesian analysis of paired high-throughput sequencing data with a beta-binomial distribution

(2013) Thomas J Hardcastle et al.   BMC BIOINFORMATICS

Differential expression analysis for paired RNA-seq data

(2013) Lisa M Chung et al.   BMC BIOINFORMATICS

A comparison of methods for differential expression analysis of RNA-seq data

(2013) Charlotte Soneson et al.   BMC BIOINFORMATICS

Evaluation of read count based RNAseq analysis methods

(2013) Yan Guo et al.   BMC GENOMICS

A comparison of statistical methods for detecting differentially expressed genes from RNA-seq data

(2012) Vanessa M. Kvam et al.   AMERICAN JOURNAL OF BOTANY

Bayesian analysis of RNA sequencing data by estimating multiple shrinkage priors

(2012) M. A. Van De Wiel et al.   BIOSTATISTICS

Exploring plant transcriptomes using ultra high-throughput sequencing

(2011) L. Wang et al.   Briefings in Functional Genomics

From RNA-seq reads to differential expression results

(2011) Alicia Oshlack et al.   GENOME BIOLOGY

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Sex-specific and lineage-specific alternative splicing in primates

(2009) R. Blekhman et al.   GENOME RESEARCH

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS