AlexsLemonade / AlexsLemonade/OpenScPCA-analysis

Use CNV distributions to identify additional Ewings tumor cells

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Description

> In looking at this I am kind of curious what cell types are in the first hump in the bimodal distribution that we see in the unknown cells are for 822 and 824 when using endo-immune or immune. Using endo + immune together it looks like we might be able to pull out two groups of unknown and could actually label some of the unknown as tumor cells. That's a question for another time, but it might be pretty easy to just plot the total CNV distributions by cell type for that group and see what it looks like.

_Originally posted by @allyhawkins in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1144#pullrequestreview-2893220384_

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The goal of this issue is to explore whether we can use inferCNV results for Ewings samples to identify additional tumor cells that were not identified in the `cell-type-ewings` module.

Contributor guide

Open the contributing guide

Research direction

Start by reviewing the inferCNV results and the cell-type-ewings module for Ewings samples 822 and 824. Plot total CNV distributions by cell type for the unknown cells, comparing the endo-immune or immune groups with endo plus immune. Done means determining whether the distributions support identifying and labeling additional tumor cells.

Written by the indexing model from the issue text.

Assessment

Domain
bioinformatics
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
30/100

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