Single-Cell Biology Course 2026: Final Project

Data used for the analysis comes from a study by Frangieh et al. [1].

Project Structure

.
├── data/                             # not on github
│   ├── frangieh/ 
│   └── ReactomePathways.gmt.zip/
└── notebooks/
    ├── Analysis.ipynb
    ├── Clustering.ipynb
    ├── Condition_Classifiction.ipynb
    └── Perturbation_Prediction.ipynb

Analysis
Preliminary Analysis of the RNA and protein data, also including normalization and log1p for the RNA data.

Condition Classification
Task 1 of the final project.

Clustering
Task 2 of the final project.

Perturbation Prediction
Task 3 of the final project.

References

[1] Frangieh, C. J., Melms, J. C., Thakore, P. I., et al. (2021). Multimodal pooled Perturb-CITE-seq screens in patient models define mechanisms of cancer immune evasion. Nature Genetics, 53, 332–341. DOI