gg4way
This is the development version of gg4way; for the stable release version, see gg4way.
4way Plots of Differential Expression
Bioconductor version: Development (3.24)
4way plots enable a comparison of the logFC values from two contrasts of differential gene expression. The gg4way package creates 4way plots using the ggplot2 framework and supports popular Bioconductor objects. The package also provides information about the correlation between contrasts and significant genes of interest.
Author: Benjamin I Laufer [aut, cre], Brad A Friedman [aut]
Maintainer: Benjamin I Laufer <blaufer at gmail.com>
citation("gg4way")):
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")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("gg4way")
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("gg4way")| gg4way | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DifferentialExpression, GeneExpression, RNASeq, Sequencing, SingleCell, Software, Transcription, Visualization |
| Version | 1.11.0 |
| In Bioconductor since | BioC 3.18 (R-4.3) (3 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.3.0), ggplot2 |
| Imports | DESeq2, dplyr, edgeR, ggrepel, glue, janitor, limma, magrittr, methods, purrr, rlang, scales, stats, stringr, tibble, tidyr |
| System Requirements | |
| URL | https://github.com/ben-laufer/gg4way |
| Bug Reports | https://github.com/ben-laufer/gg4way/issues |
See More
| Suggests | airway, BiocStyle, knitr, org.Hs.eg.db, rmarkdown, testthat, vdiffr |
| 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 | gg4way_1.11.0.tar.gz |
| Windows Binary (x86_64) | gg4way_1.11.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | gg4way_1.11.0.tgz |
| macOS Binary (sonoma-arm64) | gg4way_1.11.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/gg4way |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/gg4way |
| Bioc Package Browser | https://code.bioconductor.org/browse/gg4way/ |
| Package Short Url | https://bioconductor.org/packages/gg4way/ |
| Package Downloads Report | Download Stats |