omics-analysis-examples

A collection of compact, reusable code snippets and workflow examples demonstrating common analyses in oncology genomics and transcriptomics.

Contents

• single-cell/ – QC, clustering, and visualization (R / Seurat-like analysis).
• bulk-rnaseq/ – Differential expression (DESeq2) and enrichment analysis.
• hpc-scripts/ – Shell scripts for file organization and job submission on HPC.
• pyclone-snakemake/ – Minimal Snakemake workflow for PyClone analysis.

Each directory has its own README.md explaining the context and how to run the example with toy/public data.

Why this repo?

These are self-contained examples that show coding style, workflow structure, and reproducibility practices. They use either synthetic or small public datasets for demonstration.

License

MIT (see LICENSE)