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EasyCellType

This is the development version of EasyCellType; for the stable release version, see EasyCellType.

Annotate cell types for scRNA-seq data


Bioconductor version: Development (3.19)

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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews GeneExpression, GeneSetEnrichment, SingleCell, Software
Version 1.5.3
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, vctrs (>= 0.6.4), BiocStyle
System Requirements
URL
See More
Suggests knitr, rmarkdown, testthat (>= 3.0.0), Seurat, BiocManager, devtools
Linking To
Enhances
Depends On Me
Imports Me
Suggests 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_1.5.3.tar.gz
Windows Binary EasyCellType_1.5.3.zip
macOS Binary (x86_64) EasyCellType_1.5.2.tgz
macOS Binary (arm64) EasyCellType_1.5.0.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