scToppR
This is the development version of scToppR; to use it, please install the devel version of Bioconductor.
API Wrapper for ToppGene
Bioconductor version: Development (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")):
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("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")| 1. Introduction to scToppR | HTML | R Script |
| 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 |
| Reference Manual |
Details
| biocViews | Pathways, SingleCell, Software |
| Version | 0.99.10 |
| In Bioconductor since | BioC 3.23 (R-4.6) |
| 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 |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | scToppR_0.99.10.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (big-sur-arm64) | |
| macOS Binary (sonoma-arm64) | scToppR_0.99.10.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/scToppR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/scToppR |
| Bioc Package Browser | https://code.bioconductor.org/browse/scToppR/ |
| Package Short Url | https://bioconductor.org/packages/scToppR/ |
| Package Downloads Report | Download Stats |