Table 1. Various software which can be used to prepare RNA-seq count matrices.

function	package	framework	output	DESeq2 input function
summarizeOverlaps	GenomicAlignments	R/Bioc.	SummarizedExp.	DESeqDataSet
featureCounts	Rsubread	R/Bioc.	matrix	DESeqDataSetFromMatrix
htseq-count	HTSeq	Python	files	DESeqDataSetFromHTSeq