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 (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | CellBasedAssays, GeneExpression, GeneSetEnrichment, SingleCell, Software, Transcriptomics |
| Version | 2.17.0 |
| In Bioconductor since | BioC 3.15 (R-4.2) (4.5 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 | scGate |
| Suggests Me | escape, GSABenchmark, scLANE, SCpubr |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | UCell_2.17.0.tar.gz |
| Windows Binary (x86_64) | UCell_2.17.0.zip |
| macOS Binary (big-sur-x86_64) | UCell_2.17.0.tgz |
| macOS Binary (sonoma-arm64) | UCell_2.17.0.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 |