scpviz 0.5.8a0

A package to visualize single cell proteomics (and more to come!) data

scpviz

Build & Tests:

CI Matrix Status:

Python	Ubuntu	macOS	Windows
3.11
3.8		Unsupported

macOS + Python 3.8 is unsupported due to issues with scikit-misc installation.

Documentation:

Overview

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.

• Documentation: https://gnaprs.github.io/scpviz/
• Python Package Index (PyPI): https://pypi.org/project/scpviz/

Getting started

Installation

scpviz requires Python 3.8 or later. It is distributed as a Python package and can be installed with pip.

python3 -m pip install scpviz

This will install all required dependencies, including scanpy, anndata, pandas, and common plotting libraries.

For the most up-to-date version of scpviz, clone the repository and install the package using pip:

conda create -n scpviz python=3.8 numpy pandas pip
conda activate scpviz
pip install git+https://github.com/gnaprs/scpviz.git@main --upgrade

Quickstart

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

In-depth Tutorials

For more in-depth guides on importing, filtering, plotting, and running enrichment, see the tutorials.

API Reference

Full function documentation for the pAnnData class and utility modules can be found on our documentation page.

Contributing

If you'll like to contribute to scpviz, please see the contributing guidelines. We welcome contributions from the community to help improve, expand, and document the functionality of scpviz.

License

scpviz was created by Marion Pang. It is licensed under the terms of the MIT license.