Package: UCell 2.17.1

Massimo Andreatta

UCell: Rank-based signature enrichment analysis for single-cell data

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.

Authors:Massimo Andreatta [aut, cre], Santiago Carmona [aut]

UCell_2.17.1.tar.gz
UCell_2.17.1.zip(r-4.7-any)UCell_2.17.1.zip(r-4.6-any)UCell_2.17.1.zip(r-4.5-any)
UCell_2.17.1.tgz(r-4.6-any)UCell_2.17.1.tgz(r-4.5-any)
UCell_2.17.1.tar.gz(r-4.7-any)UCell_2.17.1.tar.gz(r-4.6-any)
UCell_2.17.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
UCell/json (API)

# Install 'UCell' in R:
install.packages('UCell', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/carmonalab/ucell/issues

Datasets:

On BioConductor:UCell-2.17.1(bioc 3.24)UCell-2.16.0(bioc 3.23)

singlecellgenesetenrichmenttranscriptomicsgeneexpressioncellbasedassays

11.75 score 212 stars 3 packages 1.2k scripts 4.2k downloads 4 exports 32 dependencies

Last updated from:f778e091f1. Checks:1 NOTE, 9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE239
linux-develOK391
source / vignettesOK613
linux-releaseOK463
macos-releaseOK210
macos-oldrelOK175
windows-develOK2276
windows-releaseOK2345
windows-oldrelOK2338
wasm-releaseOK197

Exports:AddModuleScore_UCellScoreSignatures_UCellSmoothKNNStoreRankings_UCell

Dependencies:abindassortheadbeachmatBHBiobaseBiocGenericsBiocNeighborsBiocParallelcodetoolscpp11data.tableDelayedArrayformatRfutile.loggerfutile.optionsgenericsGenomicRangesIRangeslambda.rlatticeMatrixMatrixGenericsmatrixStatsRcppS4ArraysS4VectorsSeqinfoSingleCellExperimentsnowSparseArraySummarizedExperimentXVector

Gene signature scoring with UCell
Introduction | Quick start | Get some testing data | Define gene signatures | Run UCell | Pre-calculating gene rankings | Multi-core processing | Interacting with SingleCellExperiment or Seurat | Resources | References | Session Info
Rendered fromUCell_vignette_basic.Rmdusingknitr::rmarkdown

Last update: 2025-10-01
Started: 2022-02-03

Using UCell with SingleCellExperiment
Introduction | Get some testing data | Define gene signatures | Run UCell on sce object | Signature smoothing | Resources | References | Session Info
Rendered fromUCell_sce.Rmdusingknitr::rmarkdown

Last update: 2025-10-01
Started: 2022-08-05

Using UCell with Seurat
Introduction | Get some testing data | Define gene signatures | Run UCell on Seurat object | Signature smoothing | Resources | References | Session Info
Rendered fromUCell_Seurat.Rmdusingknitr::rmarkdown

Last update: 2025-10-01
Started: 2022-08-05

Some important parameters for UCell
Introduction | Load example dataset | Parameters | Positive and negative gene sets in signatures | The maxRank parameter | Handling missing genes | Chunk size | Parallelization | Signature score smoothing | Resources | References | Session Info
Rendered fromUCell_parameters.Rmdusingknitr::rmarkdown

Last update: 2025-10-01
Started: 2025-10-01