scToppR
This is the released version of scToppR; for the devel version, see scToppR.
API Wrapper for ToppGene
Bioconductor version: Release (3.23)
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.
Author: Bryan Granger [aut, cre] 
Maintainer: Bryan Granger <grangerb at musc.edu>
citation("scToppR")):Bryan Granger. scToppR: API Wrapper for ToppGene. doi:10.18129/B9.bioc.scToppR, R package version 1.0.0, https://bioconductor.org/packages/scToppR.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("scToppR")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("scToppR")| 2. Introduction to scToppR using the Airway dataset | HTML | R Script |
| 3. Introduction to scToppr with differential expression using Seurat object data | HTML | R Script |
| 1. Introduction to scToppR | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Pathways, SingleCell, Software |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.23 (R-4.6) (< 6 months) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.5.0) |
| Imports | dplyr, forcats, ggplot2, stringr, openxlsx, viridis, patchwork, utils, httr2 |
| System Requirements | |
| URL | https://github.com/BioinformaticsMUSC/scToppR |
| Bug Reports | https://github.com/BioinformaticsMUSC/scToppR |
See More
| Suggests | airway, BiocStyle, curl, DESeq2, knitr, rmarkdown, S4Vectors, SingleCellExperiment, SummarizedExperiment, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | scToppR_1.0.0.tar.gz |
| Windows Binary (x86_64) | scToppR_1.0.0.zip |
| macOS Binary (big-sur-x86_64) | scToppR_1.0.0.tgz |
| macOS Binary (sonoma-arm64) | scToppR_1.0.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/scToppR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/scToppR |
| Package Short Url | https://bioconductor.org/packages/scToppR/ |
| Package Downloads Report | Download Stats |