EasyCellType

Annotate cell types for scRNA-seq data

Bioconductor version: Release (3.20)

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 "4.4") 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")

my-vignette	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	GeneExpression, GeneSetEnrichment, SingleCell, Software
Version	1.8.0
In Bioconductor since	BioC 3.16 (R-4.2) (2 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

Suggests	knitr, rmarkdown, testthat (>= 3.0.0), Seurat, BiocManager, devtools, BiocStyle
Linking To
Enhances
Depends On Me
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Build Report	Build Report

Package Archives

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

Source Package	EasyCellType_1.8.0.tar.gz
Windows Binary (x86_64)	EasyCellType_1.8.0.zip
macOS Binary (x86_64)	EasyCellType_1.8.0.tgz
macOS Binary (arm64)	EasyCellType_1.8.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/EasyCellType
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/EasyCellType
Bioc Package Browser	https://code.bioconductor.org/browse/EasyCellType/
Package Short Url	https://bioconductor.org/packages/EasyCellType/
Package Downloads Report	Download Stats