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
So far, MNN is the best (but still very limit) algorithm for general batch effect correction method. But based on the recent paper (https://www.nature.com/articles/s41587-019-0113-3 ), in some situations, it just exhibits minor improvement than doing nothing. It's all depends on how good your data are. 