R package (compatible with SCope) to create generic .loom files and extend them with other data e.g.: SCENIC regulons, Seurat clusters and markers, ...
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...
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...