Package: UCell 2.11.1

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_2.11.1.tar.gz
UCell_2.11.1.zip(r-4.5)UCell_2.11.1.zip(r-4.4)UCell_2.11.1.zip(r-4.3)
UCell_2.11.1.tgz(r-4.4-any)UCell_2.11.1.tgz(r-4.3-any)
UCell_2.11.1.tar.gz(r-4.5-noble)UCell_2.11.1.tar.gz(r-4.4-noble)
UCell_2.11.1.tgz(r-4.4-emscripten)UCell_2.11.1.tgz(r-4.3-emscripten)
UCell.pdf |UCell.html
UCell/json (API)
NEWS

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

Peer review:

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

Datasets:

On BioConductor:UCell-2.11.1(bioc 3.21)UCell-2.10.1(bioc 3.20)

singlecellgenesetenrichmenttranscriptomicsgeneexpressioncellbasedassays

10.61 score 140 stars 2 packages 422 scripts 2.4k downloads 4 exports 43 dependencies

Last updated 2 months agofrom:10bccc9cc4. Checks:OK: 4 NOTE: 2 ERROR: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 01 2024
R-4.5-winNOTEDec 01 2024
R-4.5-linuxNOTEDec 01 2024
R-4.4-winOKDec 01 2024
R-4.4-macOKDec 01 2024
R-4.3-winOKDec 01 2024
R-4.3-macERRORDec 01 2024

Exports:AddModuleScore_UCellScoreSignatures_UCellSmoothKNNStoreRankings_UCell

Dependencies:abindaskpassassortheadBHBiobaseBiocGenericsBiocNeighborsBiocParallelcodetoolscpp11crayoncurldata.tableDelayedArrayformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangeshttrIRangesjsonlitelambda.rlatticeMatrixMatrixGenericsmatrixStatsmimeopensslR6RcppS4ArraysS4VectorsSingleCellExperimentsnowSparseArraySummarizedExperimentsysUCSC.utilsXVectorzlibbioc

Gene signature scoring with UCell

Rendered fromUCell_vignette_basic.Rmdusingknitr::rmarkdownon Dec 01 2024.

Last update: 2023-10-25
Started: 2022-02-03

Using UCell with SingleCellExperiment

Rendered fromUCell_sce.Rmdusingknitr::rmarkdownon Dec 01 2024.

Last update: 2023-10-25
Started: 2022-08-05

Using UCell with Seurat

Rendered fromUCell_Seurat.Rmdusingknitr::rmarkdownon Dec 01 2024.

Last update: 2023-10-25
Started: 2022-08-05