دورية أكاديمية
A marker gene-based method for identifying the cell-type of origin from single-cell RNA sequencing data
العنوان: | A marker gene-based method for identifying the cell-type of origin from single-cell RNA sequencing data |
---|---|
المؤلفون: | Nima Nouri, Giorgio Gaglia, Andre H. Kurlovs, Emanuele de Rinaldis, Virginia Savova |
المصدر: | MethodsX, Vol 10, Iss , Pp 102196- (2023) |
بيانات النشر: | Elsevier |
سنة النشر: | 2023 |
المجموعة: | Directory of Open Access Journals: DOAJ Articles |
مصطلحات موضوعية: | SARGENT - SignAtuRe-GEne cell aNnoTation, Science |
الوصف: | Single-cell RNA sequencing (scRNA-seq) experiments provide opportunities to peer into complex tissues at single-cell resolution. However, insightful biological interpretation of scRNA-seq data relies upon precise identification of cell types. The ability to identify the origin of a cell quickly and accurately will greatly improve downstream analyses. We present Sargent, a transformation-free, cluster-free, single-cell annotation algorithm for rapidly identifying the cell types of origin based on cell type-specific markers. We demonstrate Sargent's high accuracy by annotating simulated datasets. Further, we compare Sargent performance against expert-annotated scRNA-seq data from human organs including PBMC, heart, kidney, and lung. We demonstrate that Sargent retains both the flexibility and biological interpretability of cluster-based manual annotation. Additionally, the automation eliminates the labor intensive and potentially biased user annotation, producing robust, reproducible, and scalable outputs. • Sargent is a transformation-free, cluster-free, single-cell annotation algorithm for rapidly identifying the cell types of origin based on cell type-specific markers. • Sargent retains both the flexibility and biological interpretability of cluster-based manual annotation. • Automation eliminates the labor intensive and potentially biased user annotation, producing robust, reproducible, and scalable outputs. |
نوع الوثيقة: | article in journal/newspaper |
اللغة: | English |
تدمد: | 2215-0161 |
العلاقة: | http://www.sciencedirect.com/science/article/pii/S2215016123001966Test; https://doaj.org/toc/2215-0161Test; https://doaj.org/article/ddb0bff18b1b40dda6c78781fb78cab5Test |
DOI: | 10.1016/j.mex.2023.102196 |
الإتاحة: | https://doi.org/10.1016/j.mex.2023.102196Test https://doaj.org/article/ddb0bff18b1b40dda6c78781fb78cab5Test |
رقم الانضمام: | edsbas.A42AA210 |
قاعدة البيانات: | BASE |
تدمد: | 22150161 |
---|---|
DOI: | 10.1016/j.mex.2023.102196 |