DESeq2 hence offers to practitioners a wide set of features with state-of-the-art inferential power. Its use cases are not limited to RNA-seq data or other transcriptomics assays; rather, many kinds of high-throughput count data can be used. Other areas for which DESeq or DESeq2 have been used include chromatin immunoprecipitation sequencing assays (e.g., [40]; see also the DiffBind package [41,42]), barcode-based assays (e.g., [43]), metagenomics data (e.g., [44]), ribosome profiling [45] and CRISPR/Cas-library assays [46]. Finally, the DESeq2 package is integrated well in the Bioconductor infrastructure [11] and comes with extensive documentation, including a vignette that demonstrates a complete analysis step by step and discusses advanced use cases.
