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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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")| 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 | ||
| 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 |
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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/scToppR/ |
| Package Short Url | https://bioconductor.org/packages/scToppR/ |
| Package Downloads Report | Download Stats |