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Welcome to scpviz

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scpviz is a Python package for single-cell and spatial proteomics data analysis, built around a custom pAnnData object.
It extends the AnnData ecosystem with proteomics-specific functionality, enabling seamless integration of proteins, peptides, and relational data.

Features

  • Set up in 5 minutes

    Install scpviz with pip and get up and running in minutes

    Getting started

  • Quickstart

    Check out the quickstart guide for a run through import, basic preprocessing and quick visualization

    Quickstart

  • In-depth Tutorials

    Step-by-step guides for importing, filtering, plotting, and running enrichment.

    Tutorials

  • API Reference

    Full function documentation for pAnnData and helper utilities.

    API Reference

  • Single-cell proteomics support: Store protein and peptide quantifications in AnnData-compatible structures.
  • Relational mapping: Track protein–peptide connectivity using a dedicated RS matrix.
  • Analysis tools: Filtering, normalization, imputation, and differential expression (DE) tailored for proteomics.
  • Functional enrichment: Integrated STRING queries for GSEA and PPI networks.
  • Custom plotting: Publication-ready plots (abundance, PCA/UMAP, clustermaps, rank-quant plots, etc.).
  • API utilities: Retrieve annotations from UniProt, cache mappings, and manage large datasets efficiently.

Getting Started

Check out the quickstart guide. For more detailed examples, check out the Tutorials.

  • Developer Notes – Guidelines for contributing, testing, and extending scpviz.

scpviz is developed for research in single-cell and spatial proteomics, supporting reproducible and scalable analysis.