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 vireoSNPAlternatively, 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/vireoIn either case, add --user if you don't have the write permission for your
Python environment.
For more instructions, see the installation manual.
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.
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)