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About Vireo

This document gives an introduction and usage manual of Vireo (Variational inference for reconstructing ensemble origins), a Bayesian method to demultiplex pooled scRNA-seq data without genotype reference.

Vireo is primarily designed 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.

Tutorials

donors: vireoSNP_donors.ipynb gives example on donor deconvolution manually

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

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)