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.
- 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
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.
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)