escape
Easy single cell analysis platform for enrichment
Bioconductor version: 3.23 · Package version: 2.8.0
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("escape")Details
| Maintainer | Nick Borcherding <ncborch@gmail.com> |
| Author | Nick Borcherding [aut, cre], Jared Andrews [aut], Tobias Hoch [ctb], Alexei Martsinkovskiy [ctb] |
| License | MIT + file LICENSE |
| Bug Reports | https://github.com/BorchLab/escape/issues |
| Downloads rank | 670 |
| Source branch | RELEASE_3_23 |
| biocViews | Annotation, Classification, GeneSetEnrichment, GeneSignaling, Pathways, Sequencing, SingleCell, Software |
Documentation
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Dependencies
Depends: R (>= 4.1)
Imports: ggdist, ggplot2 (>= 3.5.0), grDevices, Matrix, MatrixGenerics, methods, stats, SummarizedExperiment, utils
Suggests: AUCell, BiocParallel, BiocStyle, DelayedMatrixStats, dplyr, fgsea, GSEABase, ggraph, ggridges, ggpointdensity, GSVA, hexbin, igraph, irlba, knitr, msigdb, patchwork, rmarkdown, rlang, scran, SeuratObject, Seurat, SingleCellExperiment, spelling, stringr, testthat (>= 3.0.0), UCell