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broadinstitute / CellBender

CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
https://cellbender.rtfd.io
BSD 3-Clause "New" or "Revised" License
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Query: Using CellBender on Multiple scRNA-seq Samples #321

Closed ryan2han closed 8 months ago

ryan2han commented 9 months ago

Hello, I'm working with multiple scRNA-seq samples. Can I aggregate them using CellRanger aggr and then apply CellBender for background RNA correction?

jpcartailler commented 8 months ago

Not the author, but the amount of ambient expression is on a per-sample basis, so it would be advisable (IMO) to run each sample separately, then merge later.

ryan2han commented 8 months ago

Thank you for your suggestion. I did proceed in that way,