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
From experience, SCTransform does not perform well unless the majority of the cells are of the same type. It will force true unique populations together with a heavy hand, whereas MNN is much more orthogonal in its changes. Seurat even has a wrapper around [fastMNN](https://htmlpreview.github.io/?https://github.com/satijalab/seurat.wrappers/blob/master/docs/fast_mnn.html).

Haven't tried the other options though, so can't speak to them.