GSABenchmark
Tools for benchmarking single-cell gene set analysis methods
Bioconductor version: 3.24 · Package version: 1.1.2
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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 (AddModuleScore, AUCell, CSOA, GSVA, JASMINE, MDT, MLM, ORA, Pagoda2, PLAGE, Singscore, SiPSiC, ssGSEA, UCell, UDT, VAM, and Zscore).
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 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | GeneExpression, GeneSetEnrichment, SingleCell, Software, Visualization |
| Package Short Url | https://bioconductor.org/packages/GSABenchmark/ |
Citation
From within R, enter citation("GSABenchmark"):
Andrei-Florian Stoica. GSABenchmark: Tools for benchmarking single-cell gene set analysis methods. doi:10.18129/B9.bioc.GSABenchmark, R package version 1.1.2, https://bioconductor.org/packages/GSABenchmark.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
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