Welcome to EasyCellType!
The `EasyCellType` package was designed to annotate the cell types for single-cell RNA sequencing data. The package provides two statistical tests for the cell type annotation: gene set enrichment analysis (GSEA) and a Fisher's exact test combining with marker expression significance. scRNA-seq data is analyzed and generates set of markers with the differential expression score. Taking the clustered markers as input, user then can specify the database and tissue to run GSEA or fisher exact test to annotate the group of cells. The annotation Results will be presented in two ways: Hard classification gives the most possible cell type for each cluster, and soft classification gives the several top possible cell types for each cluster.
Quick start
1. Generate a cell type specific marker csv file for your data that looks like
or
2. Select database (we recommend cellmarker for best accuracy, but some tissue type may only exist in panglaodb or clustermole), species, tissue and test. If you would like to use GSEA test, P value and socre type (pos, neg or std) for the test can be specified.
3. Click Run - and it is done!