DOI: 10.18129/B9.bioc.EasyCellType  

Annotate cell types for scRNA-seq data

Bioconductor version: Release (3.17)

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 1.2.0
In Bioconductor since BioC 3.16 (R-4.2) (1 year)
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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Source Package EasyCellType_1.2.0.tar.gz
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