Metadata-Version: 2.1
Name: vireoSNP
Version: 0.1.2
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|
        
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            :target: https://pypi.org/project/vireoSNP
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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
        
        
        Installation
        ============
        
        The easiest way is to install via PyPI_ by typing this line is terminal:
        
          ::
        
            pip install vireoSNP
        
        Alternatively, you can always download this repository and install manually:
        
          ::
        
            python setup.py install
        
        For more options of installation, see the full installation_.
        
        .. _PyPI: https://pypi.org/project/vireoSNP
        .. _manual: https://vireoSNP.readthedocs.io/en/latest/manual.html
        .. _installation: https://vireoSNP.readthedocs.io/en/latest/install.html
        
        
        Usage and manual
        ================
        
        Genotyping for each cell (pre-step)
        -----------------------------------
        There might be some bioinformatics efforts in this step, however, a few existing 
        software can provide a solution. There are often two steps for this:
        
        1) identify candidate SNPs: `known common SNPs`_ / freebayes_ / cellSNP_
        2) genotype candidate SNPs in each cell: cellSNP_ / vartrix_ / `bcftools mpileup`_
        
        See more introduction in the genotyping_ section.
        
        .. _known common SNPs: https://github.com/huangyh09/cellSNP#list-of-candidate-snps
        .. _freebayes: https://github.com/ekg/freebayes
        .. _cellSNP: https://github.com/huangyh09/cellSNP
        .. _vartrix: https://github.com/10XGenomics/vartrix
        .. _bcftools mpileup: http://www.htslib.org/doc/bcftools.html
        .. _genotyping: https://vireoSNP.readthedocs.io/en/latest/genotype.html
        
        
        Demultiplexing from allelic expression
        --------------------------------------
        
        This python package offers a set of utilities functions and an executable 
        command line `vireo` for donor deconvolution in any of these four situations 
        
        1) without any genotype: 
        
           ::
        
              vireo -c $CELL_DATA -N $n_donor -o $OUT_DIR
        
        2) with genotype for all samples (tag via -t: GT, GP, or PL)
        
           ::
        
              vireo -c $CELL_DATA -d $DONOR_GT_FILE -o $OUT_DIR
        
        3) with genotype for part of the samples
        
           ::
        
              vireo -c $CELL_DATA -d $DONOR_GT_FILE -o $OUT_DIR -N $n_donor 
        
        4) with genotype but not confident
        
           ::
        
              vireo -c $CELL_DATA -d $DONOR_GT_FILE -o $OUT_DIR --forceLearnGT
        
        The cell data can be any of the following two formats:
        
        * standard VCF file with variants by cells
        * a cellSNP output folder containing VCF for variants info and sparse matrices 
          `AD` and `DP`
        
        For details, see the full manual_ or type "vireo -h" for all arguments. We also 
        provide a demo.sh_ for running the test data sets in this repo.
        
        .. _manual: https://vireoSNP.readthedocs.io/en/latest/manual.html
        .. _demo.sh: https://github.com/huangyh09/vireo/blob/master/demo.sh
        
        
        Reference
        =========
        
        Yuanhua Huang, Davis J. McCarthy, and Oliver Stegle. `Vireo: Bayesian 
        demultiplexing of pooled single-cell RNA-seq data without genotype reference 
        <https://www.biorxiv.org/content/10.1101/598748v1>`_. 
        \ **bioRxiv** \ (2019): 598748.
        
Keywords: allelic expression,multiplexed single-cell RNA-seq,variantional inference
Platform: UNKNOWN
Provides-Extra: docs
