AlexsLemonade / AlexsLemonade/OpenScPCA-analysis

Cell Type Annotation of Osteosarcoma snRNA-seq Data (SCPCP000017)

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analysis
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Description

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

https://github.com/AlexsLemonade/OpenScPCA-analysis/discussions/601

### Describe the goals of this analysis module.

We expect this analysis module will contain all of the steps taken post-processing to perform cell type annotation for the Osteosarcoma snRNA-seq data (SCPCP000017).

### What software will you require?

We will perform all of the analysis in Python using scanpy and other relevant packages, unless noted otherwise.

### What will your first pull request contain?

The first pull request will be obtaining and formatting the data, and providing a list of marker genes we will be using to perform annotation.

### What computational resources will you require?

We will perform all of the analysis in the local and cloud environments we have available to us. We do not expect any additional computational resources to be necessary.

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

We hope to file this in the next two weeks.

Contributor guide

Open the contributing guide

Research direction

Start with GitHub Discussion 601 and review the proposed Osteosarcoma snRNA-seq analysis for SCPCP000017. The first milestone is to obtain and format the data in Python with scanpy and provide the marker-gene list for annotation; done means both are included in the first pull request.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
bioinformatics
Issue type
Feature
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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