scVelo cell transitions from marker gene expressing cells
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Entering edit mode
3 months ago
rbronste ▴ 420

Hi Im working with scVelo and looking to match a subset of cells in one cluster with preferential cell state transitions and what gene(s) may underlie this connection. Currently we can do the following to put in specific cells from adata and see where the velocity goes:

x, y = scv.utils.get_cell_transitions(adata, basis='umap', starting_cell=9032)
ax = scv.pl.velocity_graph(adata, c='lightgrey', edge_width=.05, show=False)
ax = scv.pl.scatter(adata, x=x, y=y, s=120, c='ascending', cmap='gnuplot', ax=ax)

Looking to refine this a bit further to identify subsets of cells in one cluster that transition to another from the RNA velocity perspective. Thanks!

enter image description here

velocity scvelo RNA • 194 views
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