Merging single-cell RNA-seq from different platforms across different conditions
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
1 answer
Hi, Marta
Two papers published this year in Nature Biotechnology solved the problem of batch effect correction between scRNA datasets:
- Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors. (https://www.nature.com/articles/nbt.4091)
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!
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