scEnrich: An online webserver for cell-type identification of scATAC-seq data through comprehensive region enrichment analysis

There are excellently annotated cell atlases for scRNA-seq currently, and there have been many works on cell type annotation of scRNA-seq data, and many methods have achieved good achievements. However, it has been noted that the extreme sparsity of scATAC-seq data often limits its power in cell-type identification. There are still few related algorithms available, and online cell type annotation tools are still lacking. The existing methods for annotating scATAC-seq rely too much on the scRNA-seq reference set, and the cell-type label accuracy needs to be improved. Therefore, we propose to use the genomic region sets enrichment analysis to specifically cell-type identification and analysis in scATAC-seq data using the online tool scEnrich (https://bio.liclab.net/scEnrich/). We have collected a large amount of genomic region sets data related to epigenetic regulation on this website, such as transcription factors, enhancers, super enhancers, etc. In addition, we have also collected part of the single-cell data set as background. At present, scEnrich supports over 13800 genomic region reference sets, covering regions of 7 different data types. This article is based on the method of genomic region sets enrichment analysis to perform LOLA analysis on the query set and background set, determine the cell types of scATAC-seq data, and provide detailed annotations on epigenetic regulation. scEnrich provides a user-friendly interface for querying and browsing interested cell types, facilitating researchers to annotate scATAC-seq data and greatly simplifying their research work, providing valuable resources for further exploration of single-cell epigenetic regulation.