Merging single-cell RNA-seq from different platforms across different conditions
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4.2 years ago
mBrio ▴ 10

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

scRNAseq single-cell merging platforms • 2.3k views
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Entering edit mode
4.2 years ago
Min Dai ▴ 160

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!

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