escape

Easy single cell analysis platform for enrichment

Introduction

Single-cell sequencing (SCS) is a fundamental technology in investigating a diverse array of biological fields. Part of the struggle with the high-resolution approach of SCS, is distilling the data down to meaningful scientific hypotheses. escape was created to bridge SCS results, either from raw counts or from popular R-based single-cell pipelines, like Seurat or SingleCellExperiment, with gene set enrichment analyses (GSEA). The escape package allows users to easily incorporate multiple methods of GSEA and offers several visualization and analysis methods. The package accesses the entire Molecular Signature Database v7.0 and enables users to select single, multiple gene sets, and even libraries to perform enrichment analysis on.

Methods of GSEA Available

Gene Set Variation Analysis (GSVA) - citation
Single-sample Gene Set Enrichment Analysis (ssGSEA) - citation
AUCell - citation
UCell -citation

More information on each method is available in the escape manual for escape.matrix() and the citation links. If using these methods, users should cite the original works as well.

Installation

Install Via GitHub

devtools::install_github("ncborcherding/escape")

Install via Bioconductor

escape v2 is available for Bioconductor users. It can be installed with the following:

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

BiocManager::install("escape")

Learning To Use escape:

Basic Usage

Running escape.matrix()

The basic function of enrichment analysis is done using the escape.matrix() function, with the user defining the method and gene.sets to use.

#Defining Gene Set To Use:
GS <- list(Bcells = c("MS4A1", "CD79B", "CD79A", "IGH1", "IGH2"),
           Tcells = c("CD3E", "CD3D", "CD3G", "CD7","CD8A"))

#Using Seurat Built-In Example:
pbmc_small <- SeuratObject::pbmc_small
  
#Running Enrichment
trial.ssGSEA <- escape.matrix(pbmc_small, 
                              method = "ssGSEA", 
                              gene.sets = GS, 
                              min.size = NULL)

runEscape()

Alternatively, runEscape() will perform the enrichment calculations as above, but also automatically amend the single-cell object with the values added as an assay, which is named via the new.assay.name parameter. This facilitates easy downstream visualization and analysis.

pbmc_small <- runEscape(pbmc_small,
                        method = "ssGSEA", 
                        new.assay.name = "escape.ssGSEA",
                        gene.sets = GS, 
                        min.size = NULL)

Vignette

A more comprehensive vignette including the visualizations, principal component analysis and differential testing is available here.

Bug Reports/New Features

If you run into any issues or bugs please submit a GitHub issue with details of the issue.

If possible please include a reproducible example. Alternatively, an example with the the Seurat pbmc_small object would be extremely helpful.

Any requests for new features or enhancements can also be submitted as GitHub issues.

Pull Requests are welcome for bug fixes, new features, or enhancements.

Citation

If using escape, please cite the article: Borcherding, N., Vishwakarma, A., Voigt, A.P. et al. Mapping the immune environment in clear cell renal carcinoma by single-cell genomics. Commun Biol 4, 122 (2021).

ncborcherding / escape