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.

News

• All release notes can be found in doc/release.rst.
• vireoSNP_donors.ipynb giving example on donor deconvolution manually
• vireoSNP_clones.ipynb giving example clone reconstruction on mitochondral mutations
• donor_match.ipynb gives example on aligning donors to other omics data or other batches

Installation

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+https://github.com/single-cell-genetics/vireo

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 https://vireoSNP.readthedocs.io 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/demo.sh.

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

Reference

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)