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UCell

Rank-based signature enrichment analysis for single-cell data

Bioconductor version: Release (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>

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")

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 2.4.0
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
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
See More
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 (64-bit only)
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 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