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Bioconductor - escape (development version)

escape

This is the development version of escape; for the stable release version, see escape.

Easy single cell analysis platform for enrichment

Bioconductor version: Development (3.22)

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.

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

Maintainer: Nick Borcherding <ncborch at gmail.com>

Citation (from within R, enter citation("escape")): Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("escape")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("escape")
Details biocViews Annotation, Classification, GeneSetEnrichment, GeneSignaling, Pathways, Sequencing, SingleCell, Software Version 2.5.4 In Bioconductor since BioC 3.12 (R-4.0) (4.5 years) License MIT + file LICENSE Depends R (>= 4.1) Imports ggdist, ggplot2 (>= 3.5.0), grDevices, Matrix, MatrixGenerics, methods, stats, SummarizedExperiment, utils System Requirements URL Bug Reports https://github.com/BorchLab/escape/issues See More 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 Linking To Enhances Depends On Me Imports Me Suggests Me Cepo Links To Me Build Report Build Report Package Archives

Follow Installation instructions to use this package in your R session.

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