Differential Analysis

8. Differential Analysis#

8.1. Input#

  • Count matrix (genes or pathways)

  • Sample metadata

8.2. Model#

Use designs such as:

~ condition + batch

8.3. Tools#

  • DESeq2 (RNA-seq style count data)

  • edgeR

  • Limma-Voom

8.4. Visualizations#

  • Volcano plots

  • Heatmaps

  • PCA / ordination

Contents