Package: UCell 2.9.0

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_2.9.0.tar.gz
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UCell_2.9.0.tgz(r-4.4-any)UCell_2.9.0.tgz(r-4.3-any)
UCell_2.9.0.tar.gz(r-4.5-noble)UCell_2.9.0.tar.gz(r-4.4-noble)
UCell_2.9.0.tgz(r-4.4-emscripten)UCell_2.9.0.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'))

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

Datasets:

sample.matrix - Sample dataset to test UCell installation

On BioConductor:UCell-2.9.0(bioc 3.20)UCell-2.8.0(bioc 3.19)

bioconductor-package

4 exports 1.69 score 42 dependencies 2 dependents

Last updated 2 months agofrom:f62e7a2425

Exports:AddModuleScore_UCell ScoreSignatures_UCell SmoothKNN StoreRankings_UCell

Dependencies:abind askpass BH Biobase BiocGenerics BiocNeighbors BiocParallel codetools cpp11 crayon curl data.table DelayedArray formatR futile.logger futile.options GenomeInfoDb GenomeInfoDbData GenomicRanges httr IRanges jsonlite lambda.r lattice Matrix MatrixGenerics matrixStats mime openssl R6 Rcpp RcppHNSW S4Arrays S4Vectors SingleCellExperiment snow SparseArray SummarizedExperiment sys UCSC.utils XVector zlibbioc

Gene signature scoring with UCell

Massimo Andreatta, Santiago J. Carmona

Rendered fromUCell_vignette_basic.Rmdusingknitr::rmarkdownon Jun 11 2024.

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

Using UCell with SingleCellExperiment

Massimo Andreatta, Santiago J. Carmona

Rendered fromUCell_sce.Rmdusingknitr::rmarkdownon Jun 11 2024.

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

Using UCell with Seurat

Massimo Andreatta, Santiago J. Carmona

Rendered fromUCell_Seurat.Rmdusingknitr::rmarkdownon Jun 11 2024.

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

Help page	Topics
Calculate module enrichment scores from single-cell data (Seurat interface)	AddModuleScore_UCell
Calculate rankings and scores for query data and given signature set	calculate_Uscore
Check genes	check_genes
Check signature names and add standard names is missing	check_signature_names
Calculate per-cell feature rankings	data_to_ranks_data_table
Smoothing scores by KNN	knn_smooth_scores
Get signature scores from pre-computed rank matrix	rankings2Uscore
Sample dataset to test UCell installation	sample.matrix
Calculate module enrichment scores from single-cell data	ScoreSignatures_UCell
Smooth signature scores by kNN	SmoothKNN SmoothKNN.Seurat SmoothKNN.SingleCellExperiment
Split data matrix into smaller sub-matrices ('chunks')	split_data.matrix
Calculate and store gene rankings for a single-cell dataset	StoreRankings_UCell
Calculate Mann Whitney U from a vector of ranks	u_stat
Calculate U scores for a list of signatures, given a rank matrix	u_stat_signature_list
UCell: Robust and scalable single-cell gene signature scoring	UCell-package UCell

Package: UCell 2.9.0

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

Gene signature scoring with UCell

Using UCell with SingleCellExperiment

Using UCell with Seurat

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)