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reconstrue / single_cell

Single cell analysis tools built to run on Jupyter, especially Colab
http://reconstrue.com
Apache License 2.0
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Dataset: 1.3m cells from 10x #23

Open JohnTigue opened 4 years ago

JohnTigue commented 4 years ago

Visualizing and Clustering 1.3M neurons

This uses the 1.3M neurons dataset from 10x Genomics. If you have at least 30 GB of memory (recently, tests indicated that memory usage could go up to 120 GB, we are investigating), run cluster.py to produce the following result producing in 6 hours on a small server using at most 2-3 2.4 GHz cores. If you subsample to 130K cells, this takes 16 min. The tSNE computation took about 4 hours using 8 cores. The clustering result is available here.