A survey of statistical software for analysing RNA-seq data

High-throughput RNA sequencing is rapidly emerging as a favourite method for gene expression studies. We review three software packages -- edgeR, DEGseq and baySeq -- from Bioconductor http://bioconductor.org for analysing RNA-sequencing data. We focus on three aspects: normalisation, statistical models and the testing employed on these methods. We also discuss the advantages and limitations of these software packages.