EasyCellType
Annotate cell types for scRNA-seq data
Bioconductor version: Release (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 |