ArticleFrontiers in genetics2020
SCSA: A Cell Type Annotation Tool for Single-Cell RNA-seq Data.
Article in Frontiers in genetics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 97 papers.
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97 citing papers in PubMed.
- Single-cell RNA sequencing reveals the dysfunctional characteristics of PBMCs in patients with type 2 diabetes mellitus.Frontiers in immunology · 2024Trial
- scPlantAnnotate: an accurate and robust transformer-based model for plant cell type annotation.Journal of advanced research · 2026Article
- Betulinic acid alleviates ankylosing spondylitis and remodels Th17/Treg-associated immune landscapes revealed by single-cell transcriptomics.Naunyn-Schmiedeberg's archives of pharmacology · 2026Article
- Data-driven identification of cell subtypes for single-cell transcriptomic data with Subtypist.Briefings in bioinformatics · 2026Article
- Monocarboxylate Transporter 2 (MCT2) Reduction Is Associated with Increased Lung Tumor Growth and Alterations in the Immune Microenvironment in a Subcutaneous Tumor Model.International journal of molecular sciences · 2026Article
- Injury-transduced oligodendrocytes modulate neuroinflammation and glial activation in diseased and non-diseased central nervous system.Nature communications · 2026Article
- Toll-like receptor 7 constrains efferocytosis in myocardial injury.Basic research in cardiology · 2026Article
- SC-framework: A robust and FAIR semi-interactive environment for single-cell resolution datasets.iScience · 2026Article
- scMapNet: Marker-based cell type annotation of scRNA-seq data via vision transfer learning with tabular-to-image transformations.Journal of advanced research · 2026Article
- mmContext: an open framework for multimodal contrastive learning of omics and text data.Bioinformatics (Oxford, England) · 2026Article
- Immune cell annotation in the single-cell studies: technologies, challenges, and integrative solutions.Immunologic research · 2026Review
- The PagDMG6341-PagWD40-PagPOLD4 Module Coordinates Base Excision Repair in '84K' Poplar (Populus alba × P. glandulosa).Plant biotechnology journal · 2026Article
- Robust integration and annotation of single-cell and spatial omics data using interpretable gene programs.Cell genomics · 2026Article
- EZH2 directs HER2+ breast cancer progression through the modulation of epithelial plasticity.EMBO reports · 2026Article
- Pathogenesis of Pulmonary Artery Remodeling: TGF-Beta Signaling and Inhibin Subunit Beta A in Group 1 and 2 Pulmonary Hypertension.Arteriosclerosis, thrombosis, and vascular biology · 2026Article
- Early life nutritional imbalance impairs colonic epithelial regeneration through gut microbiota dysbiosis and metabolic suppression.The ISME journal · 2026Article
- GPTBioInsightor-leveraging large language models for transparent scRAN-seq cell type annotations.Bioinformatics advances · 2026Article
- Integrating trajectory inference and self-explainable predictive models to explore cell state transitions in breast cancer at single-cell resolution.Frontiers in bioinformatics · 2026Article
- Multi-omics data reveal the origin of cardiac myxoma.Communications biology · 2025Article
- AP2X-1 is a negative regulator ofmBio · 2025Article
37 more citing papers are in PubMed but not listed here.
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3 authors.
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Abstract
Currently most methods take manual strategies to annotate cell types after clustering the single-cell RNA sequencing (scRNA-seq) data. Such methods are labor-intensive and heavily rely on user expertise, which may lead to inconsistent results. We present SCSA, an automatic tool to annotate cell types from scRNA-seq data, based on a score annotation model combining differentially expressed genes (DEGs) and confidence levels of cell markers from both known and user-defined information. Evaluation on real scRNA-seq datasets from different sources with other methods shows that SCSA is able to assign the cells into the correct types at a fully automated mode with a desirable precision.
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