AlexsLemonade / AlexsLemonade/OpenScPCA-analysis

Attempt to identify tumor cells in those non-ETP samples without B cells (SCPCP000003)

Open
#811 0 comments 0 reactions 0 assignees View on GitHub
analysis
Dominant language
HTML
Stars
16
Forks
24
Avg merge
3d 5h
Merged PRs (30d)
4

Description

### If you are filing this issue based on a specific GitHub Discussion, please link to the relevant Discussion.

#630

### Describe the goals of the changes to the analysis module.

The idea is to choose the best annotated sample with B cells (`SPCL000703`) and merge it with one of the samples without B cells, and correct the batch effect with Harmony, attempting to deduce the tumor/normal status of those cells from sample without B cells by the clustering pattern, if there is any.

### What will your pull request contain?

scripts for merging/batch effect corrected object and showing the umap plots of object

### Will you require additional software beyond what is already in the analysis module?

Harmony

### Will you require different computational resources beyond what the analysis module already uses?

_No response_

### If known, when do you expect to file the pull request?

~Today or tomorrow

Contributor guide

Open the contributing guide

Research direction

Start by reviewing Discussion #630 and the analysis module's existing workflows. The issue names sample SPCL000703 and the samples without B cells, and asks for scripts that merge and Harmony-correct the objects and show UMAP plots. Done means producing those scripts and plots, with the tumor/normal inference documented if clustering supports it.

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
Mostly clear
Newbie friendliness
35/100

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