EasyCellType: marker-based cell-type annotation by automatically querying multiple databases.

ABSTRACT:

Motivation

Cell label annotation is a challenging step in the analysis of single-cell RNA sequencing (scRNA-seq) data, especially for tissue types that are less commonly studied. The accumulation of scRNA-seq studies and biological knowledge leads to several well-maintained cell marker databases. Manually examining the cell marker lists against these databases can be difficult due to the large amount of available information. Additionally, simply overlapping the two lists without considering gene ranking might lead to unreliable results. Thus, an automated method with careful statistical testing is needed to facilitate the usage of these databases.

Results

We develop a user-friendly computational tool, EasyCellType, which automatically checks an input marker list obtained by

SUBMITTER: Li R 

PROVIDER: S-EPMC10049754 | biostudies-literature | 2023

REPOSITORIES: biostudies-literature