GSABenchmark

Tools for benchmarking single-cell gene set analysis methods

Bioconductor version: 3.23 · Package version: 1.0.0

GSABenchmark is a package designed for benchmarking scRNA-seq gene set analysis (scGSA) methods. It provides both traditional and novel benchmark metrics, as well as visualization tools. Currently, GSABenchmark supports 17 scGSA methods.

Installation

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

BiocManager::install("GSABenchmark")

Details

Maintainer	Andrei-Florian Stoica <andreistoica@foxmail.com>
Author	Andrei-Florian Stoica [aut, cre] (ORCID: <https://orcid.org/0000-0002-5253-0826>)
License	MIT + file LICENSE
URL	https://github.com/andrei-stoica26/GSABenchmark
Bug Reports	https://github.com/andrei-stoica26/GSABenchmark/issues
Downloads rank	47
Source branch	RELEASE_3_23
biocViews	GeneExpression, GeneSetEnrichment, SingleCell, Software, Visualization

Documentation

Introduction to GSABenchmark

Download

Source package

Dependencies

Imports: abdiv, CSOA, decoupleR, dplyr, escape, fabR, ggplot2, ggrepel, GSVA, hammers, henna, jaccard, lsa, Matrix, MLmetrics, methods, mltools, pagoda2, paletteer, reshape2, rlang, scLang, singscore, SiPSiC, stringr, stats, VAM, withr

Suggests: AUCell, BiocStyle, knitr, qs2, ranger, rmarkdown, rpart, scater, scRNAseq, scuttle, Seurat, testthat (>= 3.0.0), UCell