escape
Easy single cell analysis platform for enrichment
Bioconductor version: Release (3.20)
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.
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 "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | 2.2.1 |
| In Bioconductor since | BioC 3.12 (R-4.0) (4 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.1) |
| Imports | AUCell, BiocParallel, grDevices, dplyr, ggdist, ggplot2, ggpointdensity, GSEABase, GSVA, SingleCellExperiment, ggridges, msigdbr, stats, reshape2, patchwork, MatrixGenerics, utils, SummarizedExperiment, UCell, stringr, methods, SeuratObject, Matrix |
| System Requirements | |
| URL |
See More
| Suggests | Seurat, hexbin, scran, knitr, rmarkdown, markdown, BiocStyle, RColorBrewer, rlang, spelling, testthat (>= 3.0.0), vdiffr |
| 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_2.2.1.tar.gz |
| Windows Binary (x86_64) | escape_2.2.1.zip |
| macOS Binary (x86_64) | escape_2.2.1.tgz |
| macOS Binary (arm64) | escape_2.2.1.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 |
| Old Source Packages for BioC 3.20 | Source Archive |