Aug 12, 2020

Public workspaceISOLATING CELLS IN LOUPE BROWSER

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  • Sumeet Gupta1
  • 1Whitehead Institute
Sumeet Gupta
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Document Citation: Sumeet Gupta 2020. ISOLATING CELLS IN LOUPE BROWSER. protocols.io https://protocols.io/view/isolating-cells-in-loupe-browser-bjmwkk7e
License: This is an open access document distributed under the terms of the Creative Commons Attribution License,  which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Created: August 12, 2020
Last Modified: August 12, 2020
Document Integer ID: 40342
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Abstract
ISOLATING CELLS IN LOUPE BROWSER

ISOLATING CELLS IN LOUPE BROWSER

Within Loupe Browser, you can follow these steps to isolate species specific cells. The example below isolates human cells.


  1. Switch over to view the Feature Plot.




2. For the features, if you search for "sum", then you should see the human and mouse sums.



3. Select human sum for the y-axis, and mouse sum for the x-axis




4. Now, make both axes logarithmic.




5. The human and mouse cells should be well separated, and you can select the desired cells using the lasso tool.




6. Once you have a custom cluster of human cells, you can switch back to t-SNE visualization if you wish.