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Proxiome Analysis Template

The Proxiome Analysis Template (PAT) is a complete, reproducible Quarto/R workflow for analyzing Proximity Network Assay (PNA) data produced by nf-core/pixelator. Built on pixelatorR, it walks you from quality control through clustering and annotation, abundance and proximity analyses, and optional statistical testing and cell visualization.

How it relates to the tutorials​

The R tutorials teach each analysis step in isolation, with explanations you can reuse in your own scripts. The PAT is the complementary end-to-end template: download it, point it at your .pxl files and metadata, and adapt the decision checkpoints to your experiment.

Get started​

  • Download the template — from the latest release, download the proxiome-analysis-template-vX.Y.Z.zip asset (the minimal file set needed to run the analysis).
  • Download an example report — a rendered HTML example of the full PAT output.
  • View the repository — source, issues, and the full README with setup and run instructions.

For installation, data preparation, and how to run the modules, follow the PAT README.