text: user1771: 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?
  
  user1771: 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).
  
  Jaakkola, M. K., Seyednasrollah, F., Mehmood, A. & Elo, L. L. Comparison of methods to detect differentially expressed genes between single-cell populations. Briefings in Bioinformatics 18, 735–743 (2017).
  Finak, G. et al. MAST: A flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data. Genome Biol. 16, 1183 (2015).
  
  
original_text: 1771: <p>I am starting to run analysis for differential expression in scRNA-Seq. Which tools are available for this kind of analysis?</p>
  
  <p>Can tools for bulk RNA-Seq like <a href="https://bioconductor.org/packages/release/bioc/vignettes/DESeq/inst/doc/DESeq.pdf" rel="noreferrer">DESeq</a> be used for scRNA-Seq?</p>
   1771: <p>According to Jaakkola et al. (ref. 1):</p>
  
  <blockquote>
    <p>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.</p>
  </blockquote>
  
  <p>They also provided a summary of the comparison between 5 tools (2 designed for Single-Cell, 2 designed for bulk, 1 general): </p>
  
  <p><a href="https://i.stack.imgur.com/Q6Sj6.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/Q6Sj6.png" alt="compar"></a> </p>
  
  <p>In my case I ended up using MAST (ref. 2, <a href="https://github.com/RGLab/MAST" rel="nofollow noreferrer">github</a>).</p>
  
  <ol>
  <li>Jaakkola, M. K., Seyednasrollah, F., Mehmood, A. &amp; Elo, L. L. <a href="https://academic.oup.com/bib/article/18/5/735/2562772" rel="nofollow noreferrer">Comparison of methods to detect differentially expressed genes between single-cell populations.</a> Briefings in Bioinformatics 18, 735–743 (2017).</li>
  <li>Finak, G. et al. <a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0844-5" rel="nofollow noreferrer">MAST: A flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data.</a> Genome Biol. 16, 1183 (2015).</li>
  </ol>
  