DOI: 10.18129/B9.bioc.EasyCellType  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see EasyCellType.

Annotate cell types for scRNA-seq data

Bioconductor version: 3.16

We developed EasyCellType which can automatically examine the input marker lists obtained from existing software such as Seurat over the cell markerdatabases. Two quantification approaches to annotate cell types are provided: Gene set enrichment analysis (GSEA) and a modified versio of Fisher's exact test. The function presents annotation recommendations in graphical outcomes: bar plots for each cluster showing candidate cell types, as well as a dot plot summarizing the top 5 significant annotations for each cluster.

Author: Ruoxing Li [aut, cre, ctb], Ziyi Li [ctb]

Maintainer: Ruoxing Li <ruoxingli at outlook.com>

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biocViews GeneExpression, GeneSetEnrichment, SingleCell, Software
Version 1.0.0
In Bioconductor since BioC 3.16 (R-4.2) (< 6 months)
License Artistic-2.0
Depends R (>= 4.2.0)
Imports clusterProfiler, dplyr, forcats, ggplot2, magrittr, rlang, stats, org.Hs.eg.db, org.Mm.eg.db, AnnotationDbi
Suggests knitr, rmarkdown, testthat (>= 3.0.0), Seurat, BiocManager, devtools
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