scverse / scverse/scanpy

comparing distribution of cell types per cohort per groups

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Python
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Description

  • Additional function parameters / changed functionality / changed defaults?
  • New analysis tool: A simple analysis tool you have been using and are missing in sc.tools?
  • New plotting function: A kind of plot you would like to seein sc.pl?
  • External tools: Do you know an existing package that should go into sc.external.*?
  • Other?

...
I would like to see how to use scanpy to compare the cell types distribution per cohort per different condition. Imagine you have different disease state who have different drug exposure, so you need to compare different cell types in each cohort per each condition or drug exposure. so it id three dimension: cell types[Bcells and Tcells], disease status[CKD vs DKD] and drug exposure[absent vs non absent]

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Research direction

Start by reviewing the existing sc.tools and sc.pl APIs for analyses and plots involving cell-type distributions. Clarify the expected comparison and visualization across cell type, disease status, and drug exposure before identifying an entry point. Done would mean a defined analysis or plotting interface with documented behavior and tests or examples.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
bioinformatics, data-visualization
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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