UCell

This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see UCell.

Rank-based signature enrichment analysis for single-cell data

Bioconductor version: 3.19

UCell is a package for evaluating gene signatures in single-cell datasets. UCell signature scores, based on the Mann-Whitney U statistic, are robust to dataset size and heterogeneity, and their calculation demands less computing time and memory than other available methods, enabling the processing of large datasets in a few minutes even on machines with limited computing power. UCell can be applied to any single-cell data matrix, and includes functions to directly interact with SingleCellExperiment and Seurat objects.

Author: Massimo Andreatta [aut, cre] , Santiago Carmona [aut]

Maintainer: Massimo Andreatta <massimo.andreatta at unil.ch>

Citation (from within R, enter citation("UCell")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("UCell")

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("UCell")

1. Gene signature scoring with UCell	HTML	R Script
2. Using UCell with SingleCellExperiment	HTML	R Script
3. Using UCell with Seurat	HTML	R Script
Reference Manual	PDF
NEWS	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	CellBasedAssays, GeneExpression, GeneSetEnrichment, SingleCell, Software, Transcriptomics
Version	2.8.0
In Bioconductor since	BioC 3.15 (R-4.2) (2.5 years)
License	GPL-3 + file LICENSE
Depends	R (>= 4.3.0)
Imports	methods, data.table (>= 1.13.6), Matrix, stats, BiocParallel, BiocNeighbors, SingleCellExperiment, SummarizedExperiment
System Requirements
URL	https://github.com/carmonalab/UCell
Bug Reports	https://github.com/carmonalab/UCell/issues

Suggests	scater, scRNAseq, reshape2, patchwork, ggplot2, BiocStyle, Seurat (>= 5.0.0), SeuratObject (>= 5.0.0), knitr, rmarkdown
Linking To
Enhances
Depends On Me
Imports Me	escape, scGate
Suggests Me	SCpubr
Links To Me
Build Report	Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	UCell_2.8.0.tar.gz
Windows Binary (x86_64)	UCell_2.8.0.zip (64-bit only)
macOS Binary (x86_64)	UCell_2.8.0.tgz
macOS Binary (arm64)	UCell_2.8.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/UCell
Source Repository (Developer Access)	git clone [email protected]:packages/UCell
Bioc Package Browser	https://code.bioconductor.org/browse/UCell/
Package Short Url	https://bioconductor.org/packages/UCell/
Package Downloads Report	Download Stats