cell type/tumor annotation for ETP T-ALL (SCPCP000003)

[UTSouthwesternDSSR]

Please link to the GitHub Discussion for this proposed analysis.

#629

Describe the goals of this analysis module.

The goal is to annotate cell type and tumor/normal status for each ETP T-ALL samples (n=31) in SCPCP000003. I followed the same analysis module, as proposed in non-ETP T-ALL (Issues: #761 and #787):

• using SAM algorithm to separate the cells
• ScType for cell type annotation using the same marker list
• CopyKat for identification of malignant cells based on the profile of genome-wide aneuploidy

What software will you require?

• R (4.2.3)
• Main packages: Seurat, reticulate, SAM, ScType, CopyKat

What will your first pull request contain?

• Creating a module skeleton
  ./create-analysis-module.py cell-type-ETP-ALL-03 --use-r --use-renv --use-conda --conda-file-only
• Adding analysis code for 00-01_processing_rds.R, 02-03_annotation.R, and multipanel_plot.R

What computational resources will you require?

I am using a standard-4XL virtual machine via AWS Lightsail for Research.

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

~Today or tomorrow