I am starting to run analysis for differential expression in scRNA-Seq. Which tools are available for this kind of analysis?
Can tools for bulk RNA-Seq like DESeq be used for scRNA-Seq?
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According to Jaakkola et al. (ref. 1):
Based on our comparisons, DESeq and Limma without any modifications are not suitable for scRNA-seq data analysis, and yet, they have performed well in the context of bulk RNA-seq data.
They also provided a summary of the comparison between 5 tools (2 designed for Single-Cell, 2 designed for bulk, 1 general):
In my case I ended up using MAST (ref. 2, github).