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====================================================== 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.

.. _cardelino: https://github.com/PMBio/cardelino .. _vireoSNP: https://pypi.org/project/vireoSNP

News

• All release notes can be found in doc/release.rst_.
• Notebook_ for subclone reconstructing with mitochrondrial mutations

.. _release.rst: https://github.com/single-cell-genetics/vireo/blob/master/doc/release.rst .. _Notebook: https://vireosnp.readthedocs.io/en/latest/vireoSNP_clones.html

Installation

Vireo is available through PyPI_. To install, type the following command line, and add -U for upgrading:

.. code-block:: bash

pip install -U vireoSNP

Alternatively, you can install from this GitHub repository for latest (often development) version by following command line

.. code-block:: bash

pip install -U git+https://github.com/single-cell-genetics/vireo

In either case, add --user if you don't have the write permission for your Python environment.

For more instructions, see the installation_ manual.

.. _PyPI: https://pypi.org/project/vireoSNP .. _installation: https://vireoSNP.readthedocs.io/en/latest/install.html

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.

.. _demultiplex usage: https://vireoSNP.readthedocs.io/en/latest/manual.html .. _demo.sh: https://github.com/huangyh09/vireo/blob/master/examples/demo.sh .. _genotyping: https://vireoSNP.readthedocs.io/en/latest/genotype.html

Reference

Yuanhua Huang, Davis J. McCarthy, and Oliver Stegle. Vireo: Bayesian demultiplexing of pooled single-cell RNA-seq data without genotype reference <https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1865-2>_. \ Genome Biology \ 20, 273 (2019)