Celltype annotation for non-ETP ALL (SCPCP000003)

[UTSouthwesternDSSR]

Please link to the GitHub Discussion for this proposed analysis.

#630

Describe the goals of this analysis module.

The goal of this analysis is to perform cell type annotation for non-ETP ALL samples in the portal.

Here are the steps taken:

00. Pre-processing the provided SCE objects

• Formatting SCE objects to Seurat objects for downstream analysis
• Setting the filter of percent.mt < 25
• Features processing: (1) dropping features with 0 counts across all cells and (2) selecting feature that is curated and has the highest count for those features that have multiple gene_IDs mapping to single gene_symbols. For multi-mapped features, features with gene_IDs starting from LINC*, SNO*, U*, and Y_RNA are dropped. These steps lead to a (3) unique mapping of gene_ID to gene_symbols.
• Doublet removal (using annotation from ALSF)

01. Feature selection/dimensionality reduction

• Using self-assembling manifold algorithm, which is a soft feature selection strategy for better separation of more homogenous populations

02. Cell type annotation with marker genes

• Using ScType to annotate cell type with markers from Azimuth reference (Human - Bone Marrow) and cancer marker from immune system in ScType database

03. Tumor cell identification

• Using CopyKat to identify genome-wide aneuploidy in single cell for distinguishing tumor cells from normal cells, by providing annotated B cells as normal cells

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-nonETP-ALL-03 --use-r --use-renv --use-conda --conda-file-only

• Adding analysis code for 00. Pre-processing the provided SCE objects

What computational resources will you require?

I am currently using our own computing system for the analysis. I may need help in transferring files or large objects, if there is any issue encountered in the future.

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

~ 09/20/2024