UCell

This is the released version of UCell; for the devel version, see UCell.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15

Rank-based signature enrichment analysis for single-cell data

Bioconductor version: Release (3.23)

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] ORCID: 0000-0002-8036-2647 , Santiago Carmona [aut] ORCID: 0000-0002-2495-0671

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

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

Massimo Andreatta, Santiago Carmona. UCell: Rank-based signature enrichment analysis for single-cell data. doi:10.18129/B9.bioc.UCell, R package version 2.16.0, https://bioconductor.org/packages/UCell.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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")

4. Some important parameters for UCell	HTML	R Script
2. Using UCell with SingleCellExperiment	HTML	R Script
3. Using UCell with Seurat	HTML	R Script
1. Gene signature scoring with UCell	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	2.16.0
In Bioconductor since	BioC 3.15 (R-4.2) (4.5 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	scGate
Suggests Me	escape, GSABenchmark, scLANE, SCpubr
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	UCell_2.16.0.tar.gz
Windows Binary (x86_64)	UCell_2.16.0.zip (64-bit only)
macOS Binary (big-sur-x86_64)	UCell_2.16.0.tgz
macOS Binary (sonoma-arm64)	UCell_2.16.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/UCell
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/UCell
Package Short Url	https://bioconductor.org/packages/UCell/
Package Downloads Report	Download Stats