Differential expression analysis tool for single cell RNA-seq data

Question

[tunl]

I am looking for the best available differential expression analysis tool for single cell RNA-seq data.

From the literatures that did some comparisons, I found that MAST, ROTS, SCDE, DEGseq, D3E, and SAMseq seem to have good performance. Which one would you recommend based on your actual experience (most accurate, reliable, and stable tool)?

I’d greatly appreciate your advice.

Thank you very much!

Answer 1

[lessismore]

Hey man, check this, its very fresh! >> https://hemberg-lab.github.io/scRNA.seq.course/index.html

[tunl]

This is great! Thank you so much! Monocle vs. MAST, which one do you think is better? Thanks a lot!

Answer 2

[theobroma22]

You can also search the RNA-seq blog:

http://www.rna-seqblog.com/powsimr-power-analysis-for-bulk-and-single-cell-rna-seq-experiments/?utm_source=RNA-Seq+Blog+Subscribers

[tunl]

Thanks so much for the information!

Answer 3

[ashotmarg2004]

I am also new to this field but here are some useful link I've found that might be useful for whoever ends up in here:

• https://www.sc-best-practices.org/preamble.html
• https://blog.bioturing.com/2022/04/18/the-maze-of-differential-gene-expression-analysis-in-single-cell-rna-seq/