vireoSNP - donor deconvolution for multiplexed scRNA-seq data
vireo: donor deconvolution for pooled single-cell data
Vireo: Variational Inference for Reconstructing Ensemble Origin by expressed SNPs in multiplexed scRNA-seq data.
Vireo is available through PyPI. To install, type the following command line, and add -U for upgrading:
pip install vireoSNP
Alternatively, you can download or clone this repository and type python setup.py install to install. In either case, add --user if you don’t have the permission as a root or for your Python environment.
For more instructions, see the installation manual.
Manual and examples
Test example data is included in this repo and demos can be found in demo.sh.
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. bioRxiv (2019): 598748.
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