Cannot use Integrated data in SCENIC

aertslab / SCENIC

SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.

http://scenic.aertslab.org

GNU General Public License v3.0

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Cannot use Integrated data in SCENIC #234

Closed Lumskie closed 2 years ago

Lumskie commented 2 years ago

Hi!! I am trying to use Seurat Integrated object in SCENIC to infer GRN. However as integration gives 2000 anchors in the data that is only getting added in the exprMat which is affecting the data. How do I work with integrated seurat object in SCENIC?

Thanks in advance!!

s-aibar commented 2 years ago

Sorry @Lumskie , I think I don't understand the question... Could you give us an example of what kind of input are you trying to provide? (e.g. maybe from Seurat tutorial?)