DESeq2

DESeq2 is available on Bioconductor and is maintained by Michael Love. It is an R library that estimates the mean-dependent variance in count data from high-throughput sequencing.

It allows for performing PCA among sample data to identify the closest samples.

Here the reference manual, and an exemple of RNAseq data treatment.

For RNA-seq data, DESeq2 is used in part 5, statistics. The data used for DESeq2 are the aligned transcripts and quantified values of differential genome expression for the different samples.

Figure1 : simplified RNAseq pipeline.