Nicolaas Van Renne

Reproduce clusters

2

Dear all, Is there any way to reproduce the clusters in the paper (MacParland et al, Nat comm), starting out from the UMI file on GSE database? (GSE115469_Data.csv) If I...

Can densMAP (in development version of Seurat) yield reproducible clustering?

3

I"m running densMAP in the development version of Seurat, and it seems to work (hallelujah!) but the clustering is not reproducible. If I run the same pipeline twice over, the...

TypeError: clone_overlap() got an unexpected keyword argument 'colorby'

1

### Description of the bug I am running the tutorial V(D)J analysis. When I run `ddl.tl.clone_overlap(adata, groupby="leiden", colorby="leiden", weighted_overlap=True) ` I get this error: Traceback (most recent call last): File...