HNSCC_code

Code for selected plots and data analyses in the HNSCC project.

This repository contains scripts used in generating specific visualizations and performing analytical steps related to the study of Head and Neck Squamous Cell Carcinoma (HNSCC). scRNA-seq data share link: https://drive.google.com/file/d/1ujzB4xCDoeaFC6e-6JFtHbJ6W270GhBa/view?usp=drive_link

Repository Structure

The repository includes two main folders:

• python_scripts/: Contains code written in Python, used for tasks such as:

  • Single-cell RNA-seq preprocessing
  • Dimensionality reduction and clustering (e.g., UMAP, PCA)
  • Visualization (e.g., violin plots, dot plots)
  • Enrichment analysis
  • Non-negative Matrix Factorization (NMF)-based module detection
  • Spatial transcriptomics analysis (e.g., cell type deconvolution)

• R_scripts/: Contains code written in R, used for:

  • Visualization
  • NicheNetR