Dear all, 

referring to the batch correction methods for scRNA-seq, would you have any preference and/or comments ? among possible choices : 

-- MNNCorrect, as outlined in SimpleSingleCell workflows : 

https://bioconductor.org/packages/release/workflows/html/simpleSingleCell.html

-- ZINB-WAVE : 

https://bioconductor.org/packages/release/bioc/html/zinbwave.html

-- HARMONY : 

https://www.biorxiv.org/content/10.1101/461954v2

-- SCTransform :

https://satijalab.org/seurat/v3.0/integration.html 

thanks a lot, 

bogdan
The results seem to be very experiment-specific. For example, in today's [SCRIBE pre-print][1], all the methods (except the one introduced) perform poorly:

![enter image description here][2]

One thing to notice is that they all fail in different ways, so the problems don't seem to be due to some artifact in the data itself. For example, MNN mixes NF and TH, but Seurat splits PEP.

  [1]: https://www.biorxiv.org/content/10.1101/793463v2
  [2]: https://user-images.githubusercontent.com/6363505/66263486-70484680-e7c1-11e9-99ee-a0cb9bcd05db.png