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Bioconductor - UCell (development version)

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 (3.22)

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")): Installation

To install this package, start R (version "4.5") 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")
Details biocViews CellBasedAssays, GeneExpression, GeneSetEnrichment, SingleCell, Software, Transcriptomics Version 2.13.1 In Bioconductor since BioC 3.15 (R-4.2) (3 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 See More 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, SCpubr Links To Me Build Report Build Report Package Archives

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

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