rSeqDiff: Detecting Differential Isoform Expression from RNA-Seq Data Using Hierarchical Likelihood Ratio Test

High-throughput sequencing of transcriptomes (RNA-Seq) has recently become a powerful tool for the study of gene expression. Researchers from the University of Michigan present rSeqDiff, an efficient algorithm for the detection of differential expression and differential splicing of genes from RNA-Seq experiments across multiple conditions. Unlike existing approaches which detect differential expression of transcripts, their approach considers three cases for each gene: 1) no differential expression, 2) differential expression without differential splicing and 3) differential splicing. The researchers specify statistical models characterizing each of these three cases and use hierarchical likelihood ratio test for model selection. Simulation studies show that this approach achieves good power for detecting differentially expressed or differentially spliced genes. Comparisons with competing methods on two real RNA-Seq datasets demonstrate that this approach provides accurate estimates of isoform abundances and biological meaningful rankings of differentially spliced genes.

rna-seq

Availability – The proposed approach is implemented as an R package named rSeqDiff – http://www-personal.umich.edu/~jianghui/rseqdiff/

Shi Y, Jiang H (2013) rSeqDiff: Detecting Differential Isoform Expression from RNA-Seq Data Using Hierarchical Likelihood Ratio Test. PLoS ONE 8(11), e79448. [article]