Metadata-Version: 2.1
Name: vireoSNP
Version: 0.5.5
Summary: vireoSNP - donor deconvolution for multiplexed scRNA-seq data
Home-page: https://github.com/huangyh09/vireoSNP
Author: Yuanhua Huang
Author-email: yuanhua@ebi.ac.uk
License: Apache-2.0
Description: |PyPI| |Docs| |Build Status| |DOI|
        
        .. |PyPI| image:: https://img.shields.io/pypi/v/vireoSNP.svg
            :target: https://pypi.org/project/vireoSNP
        .. |Docs| image:: https://readthedocs.org/projects/vireosnp/badge/?version=latest
           :target: https://vireoSNP.readthedocs.io
        .. |Build Status| image:: https://travis-ci.org/single-cell-genetics/vireo.svg?branch=master
           :target: https://travis-ci.org/single-cell-genetics/vireo
        .. |DOI| image:: https://zenodo.org/badge/187803798.svg
           :target: https://zenodo.org/badge/latestdoi/187803798
        
        
        ======================================================
        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_.
        
        .. _release.rst: https://github.com/single-cell-genetics/vireo/blob/master/doc/release.rst
        
        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)
        
Keywords: allelic expression,multiplexed single-cell RNA-seq,variantional inference
Platform: UNKNOWN
Provides-Extra: docs
