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.
News
All release notes can be found in doc/release.rst.
Notebook for subclone reconstructing with mitochrondrial mutations
Installation
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.
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)
1 maintainer
Metadata
1 maintainer
Release files for vireoSNP 0.5.9
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
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| vireosnp-0.5.9.tar.gz | 1.9 MB | Details |
Release files / vireosnp-0.5.9.tar.gz
| Download URL | vireosnp-0.5.9.tar.gz |
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| Size | 1.9 MB |
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