{ "info": { "author": "Yuanhua Huang", "author_email": "yuanhua@ebi.ac.uk", "bugtrack_url": null, "classifiers": [], "description": "|PyPI| |Docs| |Build Status|\n\n.. |PyPI| image:: https://img.shields.io/pypi/v/vireoSNP.svg\n :target: https://pypi.org/project/vireoSNP\n.. |Docs| image:: https://readthedocs.org/projects/vireosnp/badge/?version=latest\n :target: https://vireoSNP.readthedocs.io\n.. |Build Status| image:: https://travis-ci.org/huangyh09/vireo.svg?branch=master\n :target: https://travis-ci.org/huangyh09/vireo\n\n\n======================================================\nvireo: donor deconvolution for pooled single-cell data\n======================================================\n\nVireo: Variational Inference for Reconstructing Ensemble Origin by expressed \nSNPs in multiplexed scRNA-seq data. \n\nThe name vireo follows the theme from cardelino_ (for clone deconvolution), \nwhile the Python package name is vireoSNP_ to aviod name confilict on PyPI.\n\n.. _cardelino: https://github.com/PMBio/cardelino\n.. _vireoSNP: https://pypi.org/project/vireoSNP\n\n\nInstallation\n============\n\nVireo is available through PyPI_. To install, type the following command \nline, and add ``-U`` for upgrading:\n\n.. code-block:: bash\n\n pip install vireoSNP\n\nAlternatively, you can download or clone this repository and type \n``python setup.py install`` to install. In either case, add ``--user`` if you \ndon't have the permission as a root or for your Python environment.\n\nFor more instructions, see the installation_ manual.\n\n.. _PyPI: https://pypi.org/project/vireoSNP\n.. _installation: https://vireoSNP.readthedocs.io/en/latest/install.html\n\n\nManual and examples\n===================\n\nThe full manual is at https://vireoSNP.readthedocs.io \nIt includes more details on installation, `demultiplex usage`_, and preprocess \nwith genotyping_ cells.\n\nTest example data is included in this repo and demos can be found in demo.sh_.\n\nAlso, type ``vireo -h`` for all arguments with the version you are using.\n\n.. _demultiplex usage: https://vireoSNP.readthedocs.io/en/latest/manual.html\n.. _demo.sh: https://github.com/huangyh09/vireo/blob/master/demo.sh\n.. _genotyping: https://vireoSNP.readthedocs.io/en/latest/genotype.html\n\n\nReference\n=========\n\nYuanhua Huang, Davis J. 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