ArticleScience advances2022
scAllele: A versatile tool for the detection and analysis of variants in scRNA-seq.
Article in Science advances, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- A single-cell lens into the co-evolution of genotypes and phenotypes in cancer.Nature reviews. Cancer · 2026Review
- A scalable framework for single-cell eQTL mapping uncovers genetic regulators of meat production traits in pigs.Journal of animal science and biotechnology · 2026Article
- Long-read RNA-seq demarcates cis- and trans-directed alternative RNA splicing.Nature communications · 2025Article
- Identification of malignant cells in single-cell transcriptomics data.Communications biology · 2025Review
- scVAR: integrating genomics and transcriptomics from single-cell RNA-seq -insights from leukemia case studies.Frontiers in genetics · 2025Article
- Variant Impact Predictor database (VIPdb), version 2: trends from three decades of genetic variant impact predictors.Human genomics · 2024Article
- Deciphering tumour microenvironment and elucidating the origin of cancer cells in ovarian clear cell carcinoma.bioRxiv : the preprint server for biology · 2024Article
- CanCellVar: A database for single-cell variants map in human cancer.American journal of human genetics · 2024Article
- Variant Impact Predictor database (VIPdb), version 2: Trends from 25 years of genetic variant impact predictors.bioRxiv : the preprint server for biology · 2024Article
- Single-nucleotide variant calling in single-cell sequencing data with Monopogen.Nature biotechnology · 2024Article
- Phertilizer: Growing a clonal tree from ultra-low coverage single-cell DNA sequencing of tumors.PLoS computational biology · 2023Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Single-cell RNA sequencing (scRNA-seq) data contain rich information at the gene, transcript, and nucleotide levels. Most analyses of scRNA-seq have focused on gene expression profiles, and it remains challenging to extract nucleotide variants and isoform-specific information. Here, we present scAllele, an integrative approach that detects single-nucleotide variants, insertions, deletions, and their allelic linkage with splicing patterns in scRNA-seq. We demonstrate that scAllele achieves better performance in identifying nucleotide variants than other commonly used tools. In addition, the read-specific variant calls by scAllele enables allele-specific splicing analysis, a unique feature not afforded by other methods. Applied to a lung cancer scRNA-seq dataset, scAllele identified variants with strong allelic linkage to alternative splicing, some of which are cancer specific and enriched in cancer-relevant pathways. scAllele represents a versatile tool to uncover multilayer information and previously unidentified biological insights from scRNA-seq data.
Identifiers
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.