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figures towards v1.0 1.3M Mar 29, 2018
results added 1.3M clustering result Nov 5, 2018 added 1.3M clustering result Nov 5, 2018 updated cluster script Jul 16, 2018 updated info on 1M example Mar 31, 2018
cluster_20K.ipynb updated 20K neurons dataset Jul 18, 2018
logfile_1.3M.txt added PAGA to logfile of 1.3M May 21, 2018
logfile_130K.txt renamed logfile Mar 31, 2018
plot.ipynb updated plot.ipynb Feb 4, 2018

First compiled: May 22, 2017. Updated: March 28, 2018.
Thanks to M. Lotfollahi for running some of these computations!

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, run 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.

For simply plotting precomputed results on your laptop, use plot.ipynb, which does not require much memory.

For quick tests, see cluster_20K.ipynb for a notebook that processes dataset that has been subsampled to 20K by 10x.