celltype/tumor annotation for non-ETP T-ALL (SCPCP000003)

[UTSouthwesternDSSR]

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#630

Describe the goals of the changes to the analysis module.

The goal is to annotate cell type and tumor/normal status for each non-ETP T-ALL samples in SCPCP000003.

1. Marker genes are mostly obtained from the Azimuth reference (Human - Bone Marrow), with additional annotation from other sources (cancer cell and erythroid precursor from ScType database; blast cell from Bhasin et al.)
2. Based on the marker genes, we annotate cell type with ScType.
3. From the cell type annotation, we provide 'B cells' as the normal cells for CopyKat to identify tumor cells.

What will your pull request contain?

This PR will contain codes for running ScType and CopyKat as well as the documentation for corresponding results.

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

I have installed libraries needed for ScType and CopyKat in previous PR.

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

I have been using a standard-4XL virtual machine, but it runs pretty slow for CopyKat by providing one core at a time. So I ran the CopyKat analysis part on our lab server.

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

~ 10/7/2024