EasyCellType
This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see EasyCellType.
Annotate cell types for scRNA-seq data
Bioconductor version: 3.17
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 "4.3") 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 | ||
| NEWS | Text |
Details
| biocViews | GeneExpression, GeneSetEnrichment, SingleCell, Software |
| Version | 1.2.0 |
| 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 |
See More
| Suggests | knitr, rmarkdown, testthat (>= 3.0.0), Seurat, BiocManager, devtools |
| 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_1.2.0.tar.gz |
| Windows Binary | EasyCellType_1.2.0.zip |
| macOS Binary (x86_64) | EasyCellType_1.2.0.tgz |
| macOS Binary (arm64) | EasyCellType_1.2.0.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 |
| Old Source Packages for BioC 3.17 | Source Archive |