Merging single-cell RNA-seq from different platforms across different conditions

Question

[mBrio]

Hi everybody!

Is it possible to merge data from single-cell RNA-seq obtained with different platforms (e.g. Dropseq and 10X) across different conditions (e.g. tumor and reference tissue)? If yes, which methods are available?

Thanks for your help!!

Marta

Answer 1

[Min Dai]

Hi, Marta

Two papers published this year in Nature Biotechnology solved the problem of batch effect correction between scRNA datasets:

1. Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors. (https://www.nature.com/articles/nbt.4091)

2. Integrating single-cell transcriptomic data across different conditions, technologies, and species. (http://www.nature.com/articles/nbt.4096)

   Both of them offered R packages, and you can have a try!