DSRCT Dataset Analysis (SCPCP000013) #583

[danhtruong]

Please link to the GitHub Discussion for this proposed analysis.

https://github.com/AlexsLemonade/OpenScPCA-analysis/discussions/583

Describe the goals of this analysis module.

This analysis aims to annotate the DSRCT samples in the SCPCP000013 (n=7) dataset.

To do so, we will:

• Assess the quality of the data set
• Curate a list of marker genes associated with DSRCT cells
• Detect the expression levels of DSRCT marker genes in the data set
• Identify clusters in the DSRCT samples
• Use the list of marker genes to identify tumor cells
• Perform copy number inference to identify tumor cells
• Annotate normal cells
• Perform clustering on tumor cells and identify tumor cell states

What software will you require?

The analysis will be done in R using the Seurat, SingleCellExperiment, and scran packages.

What will your first pull request contain?

The first pull request will be obtaining and formatting the data, assesing the quality of the data and investigating the expression of DSRCT specific genes.

What computational resources will you require?

This will be done on a local machine.

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

No response

[Jen-OMalley]

Hi @danhtruong! I'm just sending a quick note to let you know the Data Lab team will be out of the office for a training workshop from August 19-22. We will be slower to respond during that time. While we're away, we will do our best to answer any questions or comments as soon as possible. Thank you!