velocyto-notebooks

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Hi, Where do i get "TSNE1", "TSNE2", ClusterName, Clusters ? I understand that these may be pro-computed for a data. Can you give an example of the structure / contents...

somnathtagore

Analysis Pipeline : calculate_grid_arrows()

1

When i run the analysis for dentategyrus notebook, after calculating the calculate_grid_arrows() function, i get a return of flow_grid (np.ndarray) – the gridpoints. Why this array does not have any...

shaaaarpy

mutli samples

3

Dear, Does velocyto support mutli samples ? I have nine 10x samples (nine .bam files) at different development stage, could I run them together with veloctyo ?

wangjiawen2013

Hi, running knn_imputation with this line vlm.knn_imputation(n_pca_dims=9, k=k, balanced=True, b_sight=k*6, b_maxl=int(k*3.5), n_jobs=16) I get this error AttributeError: 'VelocytoLoom' object has no attribute 'U_sz' What am I missing? Thanks a lot...

andreariba

cell cycle genes

1

Hi, I'm trying to map velocity vectors onto my existing UMAP/t-SNE embeddings. These embeddings were generated without the effect of cell cycle genes (I tried a few suboptimal ways to...

yueqiw