• Hayat, Sikander

Abstract

<jats:title>Abstract</jats:title><jats:sec><jats:title>Summary</jats:title><jats:p>Accurately identifying cell types is a critical step in single-cell sequencing analyses. Here, we present marker-based automatic cell-type annotation (MACA), a new tool for annotating single-cell transcriptomics datasets. We developed MACA by testing four cell-type scoring methods with two public cell-marker databases as reference in six single-cell studies. MACA compares favorably to four existing marker-based cell-type annotation methods in terms of accuracy and speed. We show that MACA can annotate a large single-nuclei RNA-seq study in minutes on human hearts with ∼290K cells. MACA scales easily to large datasets and can broadly help experts to annotate cell types in single-cell transcriptomics datasets, and we envision MACA provides a new opportunity for integration and standardization of cell-type annotation across multiple datasets.</jats:p></jats:sec><jats:sec><jats:title>Availability and implementation</jats:title><jats:p>MACA is written in python and released under GNU General Public License v3.0. The source code is available at https://github.com/ImXman/MACA.</jats:p></jats:sec><jats:sec><jats:title>Supplementary information</jats:title><jats:p>Supplementary data are available at Bioinformatics online.</jats:p></jats:sec>

Topics

• impedance spectroscopy
• size-exclusion chromatography