Osteosarcoma SCPCAB0027 - Tumor versus Normal cell differentiation and annotation

[rs25-code]

Please link to the GitHub Discussion for this proposed analysis.

Discussion #1117

Describe the goals of this analysis module.

This analysis module will -

• Read one of the 52 samples in Group ID SCPCAB0027, Project SCPCP000023 (Sample ID: SCPCS000758)
• Run InferCNV on the selected sample -
  • Using the Gene order file from Gencode Release 48 (GRCh38.p14)
  • Using the latest consensus cell type annotation, and the validation groups to construct normal references
• Use KMeans clustering algorithm to computationally cluster cells based on CNV score into "tumor" and "normal"
• Update the dataset with this annotation for each sample

What software will you require?

• Programming tools - RStudio, Gitkraken, R
• Packages - infercnv

What will your first pull request contain?

• The analysis module skeleton created by running create-analysis-module.py
• Some initial documentation in the README.md file

What computational resources will you require?

• No GPU needed for this analysis module
• AWS Lightsail for Research Standard-2XL instance (8 vCPUs, 32GB RAM)
• 128 GB external storage
• Laptop - Yes, analysis can be run for one sample on a laptop

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

Target: 7/7/2025