vireoSNP 0.1.5

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.

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

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 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. bioRxiv (2019): 598748.