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

example for get_clusterings output format? #38

Open
dmsalsgh97 opened this issue Nov 21, 2022 · 0 comments
Open

example for get_clusterings output format? #38

dmsalsgh97 opened this issue Nov 21, 2022 · 0 comments

Comments

@dmsalsgh97
Copy link

Hi, I'm using scenic on the seurat analyzed dataset.
So, I want to use my seurat clusters and embeddings.

As I understand, SCopeLoomR needs 2 loom file.

  1. pySCENIC output loom with auc, reg data
  2. Seurat converted loom with RNA-embeddings, clusters, markers, metadata, etc.

I currently have a problem following seurat -> SCopeLoomR converting step...
So, I want to extract cluster information for SCopeLoomR analysis (regulon heatmap, RSS plot, etc.) by directly extracting cluster information from my Seurat object.

By searching the codes, I found that SCopeLoomR uses the get_clusterings function for their downstream analysis.
In my think, if there is a tiny example dataset, I could re-format my Seurat cluster info to get_clusterings output, and run downstream analtsis without converting seurat to SCopeloomR compatible loom file...

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