AlexsLemonade / AlexsLemonade/OpenScPCA-analysis

Pilocytic Astrocytoma scRNA Analysis

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analysis
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HTML
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3d 5h
Merged PRs (30d)
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Description

### Please link to the GitHub Discussion for this proposed analysis.

[ Pilocytic Astrocytoma scRNA Analysis (Discussion #1072)](https://github.com/AlexsLemonade/OpenScPCA-analysis/discussions/1072)

### Describe the goals of this analysis module.

Annotate the Pilocytic Astrocytoma Samples within the database.

For pilocytic astrocytoma object: Following cell filtering for UMI (counts and features) and percent of mitochondrial and ribosomal genes, Seurat pipeline will be utilized performing the analysis similar to our papers: PMID: 38357919 and PMID: 39137048. Following scaling data and transformation, Harmony will be used for batch correction. Malignant and non-malignant cell will be sub clustered to increase cell cluster resolution. Further, the non-malignant cells will be sub clustered again into CD45- and CD45+. Immune cells (CD45+) will be sub clustered again into myeloid (CD68+, P2RY12+, CD11c+, CD3E-) and lymphoid (CD3E+). Reference mapping for non-malignant cell will be conducted using the following reference objects: PMID: 38357919 and PMID: 39137048

### What software will you require?

R and R Studio

### What will your first pull request contain?

The first PR will include the skeleton of the module folder and a description in the README.md file

### What computational resources will you require?

_No response_

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

_No response_

Contributor guide

Open the contributing guide

Research direction

Start with Discussion #1072 and the repository's analysis-module conventions. Create the proposed module folder and its README skeleton first, then review the stated filtering, Seurat, Harmony, sub-clustering, and reference-mapping goals. Done means the Pilocytic Astrocytoma samples are annotated through the described analysis and the module documentation explains the workflow.

Written by the indexing model from the issue text.

Assessment

Tech stack
r
Domain
bioinformatics, data
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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