UCell

DOI: 10.18129/B9.bioc.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 (3.16)

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 "4.2") 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")

 

HTML R Script Gene signature scoring with UCell
PDF   Reference Manual
Text   NEWS
Text   LICENSE

Details

biocViews CellBasedAssays, GeneExpression, GeneSetEnrichment, SingleCell, Software, Transcriptomics
Version 2.1.1
In Bioconductor since BioC 3.15 (R-4.2) (< 6 months)
License GPL-3 + file LICENSE
Depends R (>= 4.1.0)
Imports methods, data.table (>= 1.13.6), Matrix, BiocParallel, 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
Links To Me
Build Report  

Package Archives

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

Source Package UCell_2.1.1.tar.gz
Windows Binary UCell_2.1.1.zip (64-bit only)
macOS 10.13 (High Sierra) UCell_2.1.1.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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: