Closed namorosini closed 1 year ago
Do you have spliced and unspliced assays in your Seurat object? If not, you need to generate and add them to your Seurat object using velocyto.
Thank you so much! It worked!
RunPAGA with pancreas_sub occurred error:
Error in t.default(adata$layers[[k]]) : argument is not a matrix
The error is caused by using base::t instead of Matrix::t, as base::t does not support transposing sparse matrices. SCP has already ensured that it internally calls Matrix::t since a long time ago, so please make sure that you are using the latest version of SCP. @qindan2008
Hi @zhanghao-njmu @namorosini, I was able to convert my concatenated looms of different samples into 1 in Python and converted that to Seurat object. Would you mind helping me to add the spliced and unsliced (and any other info needed) from my loom-converted Seurat object to my GEX Seurat object in R? And, do I need to normalise or anything with these counts? In the typical scVelo pipeline there is normalisation before computing velocities.
Thanks so much!
Hi, I'm trying to run the SCVelo but I'm facing the following error:
Error:SystemExit: None
How can I fix that?
Thanks!