ArticleGenome biology2025
SNPmanifold: detecting single-cell clonality and lineages from single-nucleotide variants using binomial variational autoencoder.
Article in Genome biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
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Who cites it
2 citing papers in PubMed.
- Souporcell3: robust demultiplexing for high-donor single-cell RNA-seq datasets.Bioinformatics (Oxford, England) · 2026Article
- SNPmanifold: detecting single-cell clonality and lineages from single-nucleotide variants using binomial variational autoencoder.Genome biology · 2025Article
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2 authors.
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Abstract
Single-nucleotide-variant (SNV) clone assignment of high-covariance single-cell lineage tracing data remains a challenge due to hierarchical mutation structure and many missing signals. We develop SNPmanifold, a Python package that learns an SNV embedding manifold using a binomial variational autoencoder to give an efficient and interpretable cell-cell distance metric. We demonstrate that SNPmanifold is a suitable tool for analysis of complex, single-cell SNV mutation data, such as in the context of demultiplexing a large number of donors and somatic lineage tracing via mitochondrial SNV data and can reveal insights into single-cell clonality and lineages more accurately and comprehensively than existing methods.
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