EasyCellType

This package is for version 3.18 of Bioconductor; for the stable, up-to-date release version, see EasyCellType.

Annotate cell types for scRNA-seq data

Bioconductor version: 3.18

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 "4.3") 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	1.4.0
In Bioconductor since	BioC 3.16 (R-4.2) (1.5 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
System Requirements
URL

Suggests	knitr, rmarkdown, testthat (>= 3.0.0), Seurat, BiocManager, devtools
Linking To
Enhances
Depends On Me
Imports 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_1.4.0.tar.gz
Windows Binary	EasyCellType_1.4.0.zip
macOS Binary (x86_64)	EasyCellType_1.4.0.tgz
macOS Binary (arm64)	EasyCellType_1.4.0.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