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

ADD COMMENTlink 14 months ago mBrio • 10 • updated 14 months ago Minstein • 100
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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!

ADD COMMENTlink 14 months ago Minstein • 100

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