GSABenchmark
This is the development version of GSABenchmark; for the stable release version, see GSABenchmark.
Tools for benchmarking single-cell gene set analysis methods
Bioconductor version: Development (3.24)
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).
Author: Andrei-Florian Stoica [aut, cre]
Maintainer: Andrei-Florian Stoica <andreistoica at foxmail.com>
citation("GSABenchmark")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("GSABenchmark")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| Reference Manual |
Details
| biocViews | GeneExpression, GeneSetEnrichment, SingleCell, Software, Visualization |
| Version | 1.1.2 |
| In Bioconductor since | BioC 3.23 (R-4.6) (< 6 months) |
| License | MIT + file LICENSE |
| Depends | |
| 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 |
| System Requirements | |
| URL | https://github.com/andrei-stoica26/GSABenchmark |
| Bug Reports | https://github.com/andrei-stoica26/GSABenchmark/issues |
See More
| Suggests | AUCell, BiocStyle, knitr, qs2, ranger, rmarkdown, rpart, scater, scRNAseq, scuttle, Seurat, testthat (>= 3.0.0), UCell |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | |
| Windows Binary (x86_64) | GSABenchmark_1.1.2.zip |
| macOS Binary (big-sur-x86_64) | GSABenchmark_1.1.1.tgz |
| macOS Binary (sonoma-arm64) | GSABenchmark_1.1.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/GSABenchmark |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/GSABenchmark |
| Package Short Url | https://bioconductor.org/packages/GSABenchmark/ |
| Package Downloads Report | Download Stats |