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Bioconductor - EasyCellType

EasyCellType

This is the released version of EasyCellType; for the devel version, see EasyCellType.

Annotate cell types for scRNA-seq data

Bioconductor version: Release (3.21)

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>

Citation (from within R, enter citation("EasyCellType")): Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("EasyCellType")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("EasyCellType")

Details biocViews GeneExpression, GeneSetEnrichment, SingleCell, Software Version 1.10.0 In Bioconductor since BioC 3.16 (R-4.2) (2.5 years) 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, vctrs (>= 0.6.4), BiocStyle System Requirements URL See More Package Archives

Follow Installation instructions to use this package in your R session.

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