UCell

This is the development version of UCell; for the stable release version, see UCell.

Rank-based signature enrichment analysis for single-cell data

Bioconductor version: Development (3.18)

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 "4.3") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews	CellBasedAssays, GeneExpression, GeneSetEnrichment, SingleCell, Software, Transcriptomics
Version	2.5.0
In Bioconductor since	BioC 3.15 (R-4.2) (1.5 years)
License	GPL-3 + file LICENSE
Depends	R (>= 4.2.0)
Imports	methods, data.table (>= 1.13.6), Matrix, stats, BiocParallel, BiocNeighbors, SingleCellExperiment, SummarizedExperiment
Linking To
Suggests	Seurat, scater, scRNAseq, reshape2, patchwork, ggplot2, BiocStyle, knitr, rmarkdown
System Requirements
Enhances
URL	https://github.com/carmonalab/UCell
Bug Reports	https://github.com/carmonalab/UCell/issues

Depends On Me
Imports Me	escape
Suggests Me	SCpubr
Links To Me
Build Report

Package Archives

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

Source Package	UCell_2.5.0.tar.gz
Windows Binary	UCell_2.5.0.zip
macOS Binary (x86_64)	UCell_2.5.0.tgz
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/UCell
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/UCell
Bioc Package Browser	https://code.bioconductor.org/browse/UCell/
Package Short Url	https://bioconductor.org/packages/UCell/
Package Downloads Report	Download Stats