Package: escape 2.9.0

Nick Borcherding

escape: Easy single cell analysis platform for enrichment

A bridging R package to facilitate gene set enrichment analysis (GSEA) in the context of single-cell RNA sequencing. Using raw count information, Seurat objects, or SingleCellExperiment format, users can perform and visualize ssGSEA, GSVA, AUCell, and UCell-based enrichment calculations across individual cells. Alternatively, escape supports use of rank-based GSEA, such as the use of differential gene expression via fgsea.

Authors:Nick Borcherding [aut, cre], Jared Andrews [aut], Tobias Hoch [ctb], Alexei Martsinkovskiy [ctb]

escape_2.9.0.tar.gz
escape_2.9.0.zip(r-4.7)escape_2.9.0.zip(r-4.6)escape_2.9.0.zip(r-4.5)
escape_2.9.0.tgz(r-4.6-any)escape_2.9.0.tgz(r-4.5-any)
escape_2.9.0.tar.gz(r-4.7-any)escape_2.9.0.tar.gz(r-4.6-any)
escape_2.9.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
escape/json (API)

# Install 'escape' in R:

install.packages('escape', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/borchlab/escape/issues

Datasets:

escape.gene.sets - Built-In Gene Sets for escape

On BioConductor:escape-2.9.0(bioc 3.24)escape-2.8.0(bioc 3.23)

software singlecell classification annotation genesetenrichment sequencing genesignaling pathways

9.57 score 227 stars 1 packages 274 scripts 15 exports 44 dependencies

Last updated from:15bf933fef. Checks:1 WARNING, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	272
linux-devel-x86_64	OK	486
source / vignettes	OK	410
linux-release-x86_64	OK	440
macos-release-arm64	OK	194
macos-oldrel-arm64	OK	176
windows-devel	OK	346
windows-release	OK	392
windows-oldrel	OK	360
wasm-release	OK	264

Exports:densityEnrichment enrichIt enrichItPlot escape.matrix getGeneSets geyserEnrichment gseaEnrichment heatmapEnrichment pcaEnrichment performNormalization performPCA ridgeEnrichment runEscape scatterEnrichment splitEnrichment

Dependencies:abind Biobase BiocGenerics cli cpp11 DelayedArray distributional farver generics GenomicRanges ggdist ggplot2 glue gtable IRanges isoband labeling lattice lifecycle magrittr Matrix MatrixGenerics matrixStats numDeriv pillar pkgconfig quadprog R6 RColorBrewer Rcpp rlang S4Arrays S4Vectors S7 scales Seqinfo SparseArray SummarizedExperiment tibble utf8 vctrs viridisLite withr XVector

Gene-set enrichment on single-cell data with escape

Rendered fromescape.Rmdusingknitr::rmarkdown

Last update: 2026-01-04
Started: 2025-03-18

Help page	Topics
Visualize Mean Density Ranking of Genes Across Gene Sets	densityEnrichment
Flexible GSEA for Precomputed Gene Lists	enrichIt
Adaptive Visualisation of enrichIt Results	enrichItPlot
Built-In Gene Sets for escape	escape.gene.sets
Calculate Single-Cell Gene-Set Enrichment Scores	escape.matrix
Get a Collection of Gene Sets from MSigDB	getGeneSets
Visualize Enrichment Distributions Using Geyser Plots	geyserEnrichment
Classical GSEA-style Running-Enrichment Plot	gseaEnrichment
Visualize Enrichment Value Summaries Using Heatmaps	heatmapEnrichment
Visualize the PCA of Enrichment Values	pcaEnrichment
Perform Normalization on Enrichment Data	performNormalization
Perform Principal Component Analysis on Enrichment Data	performPCA
Visualize Enrichment Distributions Using Ridge Plots	ridgeEnrichment
Calculate Enrichment Scores Using Seurat or SingleCellExperiment Objects	runEscape
Plot 2D Enrichment Distributions With Density or Hexplots	scatterEnrichment
Plot Enrichment Distributions Using Split or Dodged Violin Plots	splitEnrichment

Package: escape 2.9.0

escape: Easy single cell analysis platform for enrichment

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Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)