scToppR

API Wrapper for ToppGene

Bioconductor version: 3.24 · Package version: 1.1.0

Other Bioconductor versions

devel is the development version; release is the current stable one.

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.

DOI: 10.18129/B9.bioc.scToppR

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
Source branch	devel
Build report	Bioconductor build system, r-universe
biocViews	Pathways, SingleCell, Software
Package Short Url	https://bioconductor.org/packages/scToppR/

Citation

From within R, enter citation("scToppR"):

Bryan Granger. scToppR: API Wrapper for ToppGene. doi:10.18129/B9.bioc.scToppR, R package version 1.1.0, https://bioconductor.org/packages/scToppR.

Generated from the package metadata; it may differ from the package's own citation.

Documentation

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)