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.
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
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
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
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)