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 (3.23)
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 unige.ch>
citation("UCell")):
Installation
To install this package, start R (version "4.6") 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 |
| 4. Some important parameters for UCell | HTML | R Script |
| Reference Manual |
Details
| biocViews | CellBasedAssays, GeneExpression, GeneSetEnrichment, SingleCell, Software, Transcriptomics |
| Version | 2.15.0 |
| In Bioconductor since | BioC 3.15 (R-4.2) (3.5 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 | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | UCell_2.15.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| 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 |