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stephenslab / fastTopics

Fast algorithms for fitting topic models and non-negative matrix factorizations to count data.
https://stephenslab.github.io/fastTopics
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Imported Count Matrix by Seurat, but Col Names are Cell Names #13

Closed h1hui closed 3 years ago

h1hui commented 3 years ago

I imported raw count matrix from my seurat object, using function counts <- GetAssayData(object,"counts") And then found out my column names are cell names, unlike the sample dataset. How should I continue fastTopics from my Seurat object?

pcarbo commented 3 years ago

@h1hui, Yes you should do 

counts <- t(GetAssayData(object,"counts"))

See also the fastTopics Seurat wrapper, which you can find here.

h1hui commented 3 years ago

Thanks! It solved.