This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see EasyCellType.
Bioconductor version: 3.16
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")
):
To install this package, start R (version "4.2") 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.
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("EasyCellType")
HTML | R Script | my-vignette |
Reference Manual | ||
Text | NEWS |
biocViews | GeneExpression, GeneSetEnrichment, SingleCell, Software |
Version | 1.0.0 |
In Bioconductor since | BioC 3.16 (R-4.2) (< 6 months) |
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 |
LinkingTo | |
Suggests | knitr, rmarkdown, testthat (>= 3.0.0), Seurat, BiocManager, devtools |
SystemRequirements | |
Enhances | |
URL | |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me | |
Build Report |
Follow Installation instructions to use this package in your R session.
Source Package | EasyCellType_1.0.0.tar.gz |
Windows Binary | EasyCellType_1.0.0.zip |
macOS Binary (x86_64) | EasyCellType_1.0.0.tgz |
macOS Binary (arm64) | EasyCellType_1.0.0.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 |
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