GSABenchmark
This is the development version of GSABenchmark; to use it, please install the devel version of Bioconductor.
Tools for benchmarking single-cell gene set analysis methods
Bioconductor version: Development (3.23)
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.
Author: Andrei-Florian Stoica [aut, cre]
Maintainer: Andrei-Florian Stoica <andreistoica at foxmail.com>
citation("GSABenchmark")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("GSABenchmark")
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("GSABenchmark")| GSABenchmark | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | GeneExpression, GeneSetEnrichment, SingleCell, Software, Visualization |
| Version | 0.99.6 |
| In Bioconductor since | BioC 3.23 (R-4.6) |
| 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 | GSABenchmark_0.99.6.tar.gz |
| Windows Binary (x86_64) | GSABenchmark_0.99.6.zip |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (big-sur-arm64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/GSABenchmark |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/GSABenchmark |
| Bioc Package Browser | https://code.bioconductor.org/browse/GSABenchmark/ |
| Package Short Url | https://bioconductor.org/packages/GSABenchmark/ |
| Package Downloads Report | Download Stats |