MarkerCount: A stable, count-based cell type identifier for single-cell RNA-seq experiments.

ABSTRACT: Cell type identification is a key step toward downstream analysis of single cell RNA-seq experiments. Although the primary objective is to identify known cell populations, good identifiers should also recognize unknown clusters which may represent a previously unidentified subpopulation of a known cell type or tumor cells of an unknown phenotype. Herein, we present MarkerCount, which utilizes the number of expressed markers, regardless of their expression level. MarkerCount works in both reference- and marker-based mode, where the latter utilizes existing lists of markers, while the former uses a pre-annotated dataset to find markers to be used for cell type identification. In both modes, MarkerCount first utilizes the "marker count" to identify cell populations and, after rejecting uncert

SUBMITTER: Kim H 

PROVIDER: S-EPMC9233224 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature