vidger
This is the released version of vidger; for the devel version, see vidger.
Create rapid visualizations of RNAseq data in R
Bioconductor version: Release (3.23)
The aim of vidger is to rapidly generate information-rich visualizations for the interpretation of differential gene expression results from three widely-used tools: Cuffdiff, DESeq2, and edgeR.
Author: Brandon Monier [aut, cre], Adam McDermaid [aut], Jing Zhao [aut], Qin Ma [aut, fnd]
Maintainer: Brandon Monier <brandon.monier at gmail.com>
citation("vidger")):
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("vidger")
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("vidger")| Visualizing RNA-seq data with ViDGER | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DifferentialExpression, GeneExpression, ImmunoOncology, RNASeq, Software, Visualization |
| Version | 1.32.0 |
| In Bioconductor since | BioC 3.7 (R-3.5) (8.5 years) |
| License | GPL-3 | file LICENSE |
| Depends | R (>= 3.5) |
| Imports | Biobase, DESeq2, edgeR, GGally, ggplot2, ggrepel, knitr, RColorBrewer, rmarkdown, scales, stats, SummarizedExperiment, tidyr, utils |
| System Requirements | |
| URL | https://github.com/btmonier/vidger https://bioconductor.org/packages/release/bioc/html/vidger.html |
| Bug Reports | https://github.com/btmonier/vidger/issues |
See More
| Suggests | BiocStyle, testthat |
| 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 | vidger_1.32.0.tar.gz |
| Windows Binary (x86_64) | vidger_1.32.0.zip |
| macOS Binary (big-sur-x86_64) | vidger_1.32.0.tgz |
| macOS Binary (sonoma-arm64) | vidger_1.32.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/vidger |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/vidger |
| Bioc Package Browser | https://code.bioconductor.org/browse/vidger/ |
| Package Short Url | https://bioconductor.org/packages/vidger/ |
| Package Downloads Report | Download Stats |