MarcoPolo: a method to discover differentially expressed genes in single-cell RNA-seq data without depending on prior clustering.

ABSTRACT: The standard analysis pipeline for single-cell RNA-seq data consists of sequential steps initiated by clustering the cells. An innate limitation of this pipeline is that an imperfect clustering result can irreversibly affect the succeeding steps. For example, there can be cell types not well distinguished by clustering because they largely share the global structure, such as the anterior primitive streak and mid primitive streak cells. If one searches differentially expressed genes (DEGs) solely based on clustering, marker genes for distinguishing these types will be missed. Moreover, clustering depends on many parameters and can often be subjective to manual decisions. To overcome these limitations, we propose MarcoPolo, a method that identifies informative DEGs independently of prior clu

SUBMITTER: Kim C 

PROVIDER: S-EPMC9262626 | biostudies-literature | 2022 Jul

REPOSITORIES: biostudies-literature