|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 ==== Home ==== .. :Author: Yuanhua Huang .. :Version: 0.2.0 .. :Last viewed: Jun 30, 2019 About Vireo =========== This documentation gives an introduction and usage manual of Vireo (Variational inference for reconstructing ensemble origins), a Bayesian method to demultiplex pooled scRNA-seq data with or without genotype reference. Vireo is primarily designed for demultiplexing cells into donors by modelling of expressed alleles. It supports a variety of settings of donor genotype (from entirely missing, to partially missing, to fully observed). See more details in `manual`_ section. As a general cell clustering methods by allelic ratio (equivalent to genotyping), Vireo is applicable for more settings besides donor demultiplexing, including reconstruction of somatic clones, see `vireoSNP_clones.ipynb`_ for example on mitochondral mutations. .. _manual: https://vireosnp.readthedocs.io/en/latest/manual.html Notebooks for interactive analysis ================================== Here are some notebooks for interactive analysis. Usually, you only need to use the command line to perform donor deconvolution, but you may refer to some of these notebooks for additional analysis. **donors**: `vireoSNP_donors.ipynb`_ gives example on donor deconvolution manually. The `vireo` command line does this job automatically. **donors**: `donor_match.ipynb`_ gives example on aligning donors to other omics data or other batches **clones**: `vireoSNP_clones.ipynb`_ gives example on clone reconstruction on mitochondral mutations .. _donor_match.ipynb: https://nbviewer.jupyter.org/github/single-cell-genetics/vireo/blob/master/examples/donor_match.ipynb .. _vireoSNP_donors.ipynb: https://nbviewer.jupyter.org/github/single-cell-genetics/vireo/blob/master/examples/vireoSNP_donors.ipynb .. _vireoSNP_clones.ipynb: https://nbviewer.jupyter.org/github/single-cell-genetics/vireo/blob/master/examples/vireoSNP_clones.ipynb Quick Resources =============== **Latest version on GitHub** https://github.com/single-cell-genetics/vireo **Scripts for simulation** https://github.com/single-cell-genetics/vireo/tree/master/simulate **All releases** https://pypi.org/project/vireoSNP/#history Issue reports ============= If you find any error or suspicious bug, we will appreciate your report. Please write them in the github issues: https://github.com/single-cell-genetics/vireo/issues References ========== 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) .. toctree:: :caption: Main :maxdepth: 1 :hidden: install manual genotype API release .. toctree:: :caption: Notebooks :maxdepth: 1 :hidden: vireoSNP_clones