Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

What types of clustering is required? #142

Open
JiahuaQu opened this issue Oct 13, 2023 · 0 comments
Open

What types of clustering is required? #142

JiahuaQu opened this issue Oct 13, 2023 · 0 comments

Comments

@JiahuaQu
Copy link

Hi, we are considering using the SoupX, but we are confused about the clusters requirement. Because we usually analyze single-cell data that are generated by 10X in Seurat, we didn't do the downstream analysis in CellRanger, such as clustering. We will cluster cell types in Seurat. In this case, I don't think there's any cluster information from 10X folder. However, the data should have already been processed, filtered and normalized in Seurat before clustering, so I am confused what types of count matrix (raw, normalized, scaled) and what types of clustering are required by the SoupX?
Is there any suggestion how to connect SoupX with Seurat? Thank you.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant