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], Alexei Martsinkovskiy [ctb]
Maintainer: Nick Borcherding <ncborch at gmail.com>
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")| Escape-ingToWork | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Annotation, Classification, GeneSetEnrichment, GeneSignaling, Pathways, Sequencing, SingleCell, Software |
| Version | 2.5.3 |
| 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, 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.
| Source Package | escape_2.5.3.tar.gz |
| Windows Binary (x86_64) | escape_2.5.3.zip |
| macOS Binary (x86_64) | escape_2.5.3.tgz |
| macOS Binary (arm64) | escape_2.5.3.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/escape |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/escape |
| Bioc Package Browser | https://code.bioconductor.org/browse/escape/ |
| Package Short Url | https://bioconductor.org/packages/escape/ |
| Package Downloads Report | Download Stats |