Quick Start with PNA Analysis

Looking for a full analysis template?

These tutorials cover each step in depth. For a ready-to-run end-to-end Quarto workflow, see the Proxiome Analysis Template (PAT).

Step by step tutorials R

1. Data Handling

• Loading data
• Aggregating data
• Save data

2. Quality Control

• Component filtering
• Removing outliers

3. Abundance Normalization

• The dsb normalization
• Normalize MPX

4. Data Integration

• Harmonizing data

5. Cell Annotation

• Clustering and dimensionality reduction
• Annotation by differential protein abundance
• Annotation by marker gating

6. Differential Abundance

7. Spatial Analyses

• Differential clustering analysis
• Differential colocalization analysis

8. Cell Visualization

9. Patch analysis