scToppR
API Wrapper for ToppGene
Bioconductor version: 3.24 · Package version: 1.1.0
scToppR provides an easy-to-use API wrapper for the ToppGene web platform, used for gene ontology and functional enrichment research. The package also integrates visualization tools, making it a convenient tool directly connecting ToppGene to code-based workflows in R. The tool can also easily save results into different formats.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("scToppR")Details
| Maintainer | Bryan Granger <grangerb@musc.edu> |
| Author | Bryan Granger [aut, cre] (ORCID: <https://orcid.org/0009-0008-6663-3755>) |
| License | MIT + file LICENSE |
| URL | https://github.com/BioinformaticsMUSC/scToppR |
| Bug Reports | https://github.com/BioinformaticsMUSC/scToppR |
| Downloads rank | 217 |
| Source branch | devel |
| biocViews | Pathways, SingleCell, Software |
Documentation
- Introduction to scToppR
- scToppR with differential expression, Airway dataset
- scToppR with differential expression, Seurat object data
Download
Follow the installation instructions to use this package in your R session.
| Source package | scToppR_1.1.0.tar.gz |
| Windows binary (x86_64) | scToppR_1.1.0.zip |
| macOS binary (arm64) | scToppR_1.1.0.tgz |
| macOS binary (x86_64) | scToppR_1.1.0.tgz |
Dependencies
Depends: R (>= 4.5.0)
Imports: dplyr, forcats, ggplot2, stringr, openxlsx, viridis, patchwork, utils, httr2
Suggests: airway, BiocStyle, curl, DESeq2, knitr, rmarkdown, S4Vectors, SingleCellExperiment, SummarizedExperiment, testthat (>= 3.0.0)