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genepattern / single_cell_clustering_notebook

BSD 3-Clause "New" or "Revised" License
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minor notebook + code updates #16

Closed alex-wenzel closed 5 years ago

alex-wenzel commented 5 years ago

This pull request addresses a number of tickets

SNPA-11: Benchmark time estimates

This ticket says to include benchmarks for the pancreasMouse.txt dataset, but since we are focusing on the Seurat tutorial, I decided to include benchmarks for those. To come up with the upper and lower bounds, I timed the execution on my laptop and added a healthy number of seconds to the upper bound to be safe - most of these times were closer to the lower bound.

SNPA-22: Show tSNE first in step 4

Pretty much self-explanatory. It's worth noting that this does not fix SNPA-28 or SNPA-29 so now the Heatmap is inaccessible instead of the tSNE.

SNPA-34: Make gene_x_cell a 'choice' type

Instead of True or False, users now see "gene by cell" or "cell by gene" without any changes to the backend. Hopefully that will make the input interface more user-friendly.

SNPA-16: Make regression an option

I added an extra "yes"/"no" option to step 2. I decided to include all regression as one option, but we could make separate options for cell counts and %mito regression.

edjuaro commented 5 years ago

I just checked out alexdev. Starting to review this pull request.

edjuaro commented 5 years ago

All items work as described on my test! (using the edjuaro/molecular-tumor-board:6.0 container).