DEGseq is an R package designed to identify differentially expressed genes or isoforms from RNA-seq data. It integrates three existing methods and introduces two novel methods based on MA-plot to detect and visualize gene expression differences. The package accepts uniquely mapped reads from RNA-seq data or gene expression values from other programs like RPKM. It outputs a text file with expression values, $P$-values, and $Q$-values, as well as an XHTML summary page with statistical summaries. The methods include Fisher’s exact test, likelihood ratio test, and two MA-plot-based methods that estimate noise levels using technical replicates. DEGseq supports multiple testing correction and can handle two groups of samples with replicates. The package is available at http://bioinfo.au.tsinghua.edu.cn/software/degseq.DEGseq is an R package designed to identify differentially expressed genes or isoforms from RNA-seq data. It integrates three existing methods and introduces two novel methods based on MA-plot to detect and visualize gene expression differences. The package accepts uniquely mapped reads from RNA-seq data or gene expression values from other programs like RPKM. It outputs a text file with expression values, $P$-values, and $Q$-values, as well as an XHTML summary page with statistical summaries. The methods include Fisher’s exact test, likelihood ratio test, and two MA-plot-based methods that estimate noise levels using technical replicates. DEGseq supports multiple testing correction and can handle two groups of samples with replicates. The package is available at http://bioinfo.au.tsinghua.edu.cn/software/degseq.