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.
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
Installation
Vireo is available through PyPI. To install, type the following command line, and add -U for upgrading:
pip install vireoSNPAlternatively, 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)
1 maintainer
Metadata
1 maintainer
Release files for vireoSNP 0.3.1
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-0.3.1.tar.gz | 24.5 kB | Details |
Release files / vireoSNP-0.3.1.tar.gz
| Download URL | vireoSNP-0.3.1.tar.gz |
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| Size | 24.5 kB |
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