UCell

DOI: 10.18129/B9.bioc.UCell  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see UCell.

Rank-based signature enrichment analysis for single-cell data

Bioconductor version: 3.17

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>

Installation

To install this package, start R (version "4.3") 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")

 

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

Details

biocViews	CellBasedAssays, GeneExpression, GeneSetEnrichment, SingleCell, Software, Transcriptomics
Version	2.4.0
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
LinkingTo
Suggests	Seurat, scater, scRNAseq, reshape2, patchwork, ggplot2, BiocStyle, knitr, rmarkdown
SystemRequirements
Enhances
URL	https://github.com/carmonalab/UCell
BugReports	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_2.4.0.tar.gz
Windows Binary	UCell_2.4.0.zip
macOS Binary (x86_64)	UCell_2.4.0.tgz
macOS Binary (arm64)	UCell_2.4.0.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