A step-by-step tutorial for differential expression analysis and pathway enrichment analysis using TCGA BRCA RNA-seq data.
This tutorial covers:
- Downloading TCGA RNA-seq count data from GDC
- Data preprocessing and metadata preparation
- Differential expression analysis using limma
- Volcano plot visualization
- Gene Set Enrichment Analysis (GSEA)
- GO, KEGG, and Hallmark enrichment analysis
00_download_gdc_counts.Rmd: Download TCGA BRCA RNA-seq count data and metadata from the GDC portal.
01_Preprocessing.Rmd: Preprocess count matrices and clinical metadata for downstream analysis.
02_DEG.Rmd: Perform differential expression analysis using limma.
03_Volcano.Rmd: Generate labeled and unlabeled volcano plots for DEG visualization.
04_Enrichment.Rmd: Perform GSEA enrichment analysis for:
- GO Biological Process
- KEGG pathways
- Hallmark gene sets