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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.

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Installation

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

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)

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