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.
Sweave vignettes for reproducing all figures and tables in this paper, including data objects for the experiments mentioned, and code for aligning reads and for benchmarking, can be found in a package DESeq2paper [66].
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