CytoVI

Variational inference for antibody-based single cell technologies.

CytoVI accomplishes the following analysis tasks:

• Integration/batch correction
• Differential protein expression analysis
• Label-free differential abundance analysis
• Imputation of unseen proteins from overlapping antibody panels
• Technology integration (e.g. Flow and Mass cytometry)
• RNA/modality imputation after integration of flow/mass cytometry data with CITE-seq data
• Automated cell annotation via transfer learning

Getting started

To get started please check out the basic analysis notebook in the docs.

Installation

You need to have Python 3.10 or newer installed on your system. If you don't have Python installed, we recommend installing Mambaforge.

There are several alternative options to install CytoVI:

1. Install the latest development version:

pip install git+https://github.com/florianingelfinger/CytoVI.git@main

Release notes

See the changelog.

Contact

For questions and help requests, you can reach out in the scverse discourse. If you found a bug, please use the issue tracker.

Citation

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