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vireoSNP - donor deconvolution for multiplexed scRNA-seq data

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vireo: donor deconvolution for pooled single-cell data

Vireo: Variational Inference for Reconstructing Ensemble Origin by expressed SNPs in multiplexed scRNA-seq data.

The name vireo follows the theme from cardelino (for clone deconvolution), while the Python package name is vireoSNP to aviod name confilict on PyPI.


  • All release notes can be found in doc/release.rst.
  • Notebook for subclone reconstructing with mitochrondrial mutations


Vireo is available through PyPI. To install, type the following command line, and add -U for upgrading:

pip install -U vireoSNP

Alternatively, you can install from this GitHub repository for latest (often development) version by following command line

pip install -U git+

In either case, add --user if you don’t have the write permission for your Python environment.

For more instructions, see the installation manual.

Manual and examples

The full manual is at It includes more details on installation, demultiplex usage, and preprocess with genotyping cells.

Test example data is included in this repo and demos can be found in examples/

Also, type vireo -h for all arguments with the version you are using.


Yuanhua Huang, Davis J. McCarthy, and Oliver Stegle. Vireo: Bayesian demultiplexing of pooled single-cell RNA-seq data without genotype reference. Genome Biology 20, 273 (2019)

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