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kstreet13 / slingshot

Functions for identifying and characterizing continuous developmental trajectories in single-cell data.
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slingshot took long time for 86 k cells #157

Closed FADHLyemen closed 2 years ago

FADHLyemen commented 2 years ago

How long does it take for 86k cells for slingshot? it had been running for three days and not finished yet. Is there an option to run it in multi-cores?

kstreet13 commented 2 years ago

With large datasets, Slingshot can be quite slow if you aren't careful (the runtime scales with number of cells and number of lineages). As we discussed in the vignette, we highly recommend making use of the approx_points argument to speed up the runtime. With 86k cells, this will probably make a substantial difference.