EasyCellType
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see EasyCellType.
Annotate cell types for scRNA-seq data
Bioconductor version: 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("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 | ||
NEWS | Text |
Details
biocViews | GeneExpression, GeneSetEnrichment, SingleCell, Software |
Version | 1.6.0 |
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 |
See More
Suggests | knitr, rmarkdown, testthat (>= 3.0.0), Seurat, BiocManager, devtools, BiocStyle |
Linking To | |
Enhances | |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me | |
Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | EasyCellType_1.6.0.tar.gz |
Windows Binary (x86_64) | EasyCellType_1.6.0.zip |
macOS Binary (x86_64) | EasyCellType_1.6.0.tgz |
macOS Binary (arm64) | EasyCellType_1.6.0.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 |