ArticleBioinformatics (Oxford, England)2020
scHLAcount: allele-specific HLA expression from single-cell gene expression data.
Article in Bioinformatics (Oxford, England), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 30 citations in OpenAlex.
- Single-nucleus brain transcriptomics reveals microglia dysfunction in multiple system atrophy.Nature communications · 2026Article
- DAESC + : high-performance, integrated software for single-cell allele-specific expression data.BMC bioinformatics · 2026Article
- Allele-specific immune gene quantification and expression analysis in single-cell RNA-seq data.NAR genomics and bioinformatics · 2025Article
- Quantifying HLA transcripts by genotype in chimeric mixtures at single-cell resolution.bioRxiv : the preprint server for biology · 2025Article
- Article
- Computational methods for allele-specific expression in single cells.Trends in genetics : TIG · 2024Review
- Genomic and immune heterogeneity of multiple synchronous lung adenocarcinoma at different developmental stages.Nature communications · 2024Article
- Enhanced CD95 and interleukin 18 signalling accompany T cell receptor Vβ21.3+ activation in multi-inflammatory syndrome in children.Nature communications · 2024Article
- Mapping the dynamic genetic regulatory architecture of HLA genes at single-cell resolution.Nature genetics · 2023Article
- Methods and Insights from Single-Cell Expression Quantitative Trait Loci.Annual review of genomics and human genetics · 2023Review
- Comparison between qPCR and RNA-seq reveals challenges of quantifying HLA expression.Immunogenetics · 2023Article
- Mapping the dynamic genetic regulatory architecture ofmedRxiv : the preprint server for health sciences · 2023Article
- Pervasiveness of HLA allele-specific expression loss across tumor types.Genome medicine · 2023Article
- MuSiC2: cell-type deconvolution for multi-condition bulk RNA-seq data.Briefings in bioinformatics · 2022Article
- Integration of tumor extrinsic and intrinsic features associates with immunotherapy response in non-small cell lung cancer.Nature communications · 2022Article
- Unique Molecular Identifier-Based High-Resolution HLA Typing and Transcript Quantitation Using Long-Read Sequencing.Frontiers in genetics · 2022Article
- HLA allele-specific expression: Methods, disease associations, and relevance in hematopoietic stem cell transplantation.Frontiers in immunology · 2022Review
- Allele-specific expression: applications in cancer and technical considerations.Current opinion in genetics & development · 2021Review
- HLA RNA Sequencing With Unique Molecular Identifiers Reveals High Allele-Specific Variability in mRNA Expression.Frontiers in immunology · 2021Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
summaryBulk RNA sequencing studies have demonstrated that human leukocyte antigen (HLA) genes may be expressed in a cell type-specific and allele-specific fashion. Single-cell gene expression assays have the potential to further resolve these expression patterns, but currently available methods do not perform allele-specific quantification at the molecule level. Here, we present scHLAcount, a post-processing workflow for single-cell RNA-seq data that computes allele-specific molecule counts of the HLA genes based on a personalized reference constructed from the sample's HLA genotypes. AVAILABILITY AND IMPLEMENTATION: scHLAcount is available under the MIT license at https://github.com/10XGenomics/scHLAcount. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.