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GregorySchwartz / too-many-cells

Cluster single cells and analyze cell clade relationships with colorful visualizations.
https://gregoryschwartz.github.io/too-many-cells/
GNU General Public License v3.0
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Seurat SCtransform #48

Closed dekan-aleksandr closed 1 year ago

dekan-aleksandr commented 2 years ago

Hello developers of too-many-cells! Could I use SCtranfrom normalized values as input? Does it contradict the assumptions of your algorithm?

GregorySchwartz commented 2 years ago

The underlying model uses cosine similarity between feature vectors to define similar cells. If that is not appropriate for with SCtransform, then it should not be used, but otherwise it should be fine. Just make sure to disable TooManyCells normalizations / filtering if you are already providing that.