daVis
This is the development version of daVis; to use it, please install the devel version of Bioconductor.
Visualization Of Differential Expression Analysis
Bioconductor version: Development (3.24)
This package contains utility functions to visualize the output from differential expression analysis. The input can be either a model or a list of top tables or a combination of the two. The model can be output from limma, edgeR or DESeq2.
Author: Katarzyna Gorczak [aut, cre], Laure Cougnaud [aut]
Maintainer: Katarzyna Gorczak <katarzyna.gorczak at openanalytics.eu>
citation("daVis")):
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("daVis")
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("daVis")| daVis package | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DataRepresentation, DifferentialExpression, Microarray, RNASeq, Software, Visualization |
| Version | 0.99.4 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | GPL-3 |
| Depends | |
| Imports | edgeR, ggh4x, ggplot2, grDevices, limma, plyr, stats, utils, DESeq2, rlang, legendry, UpSetR |
| System Requirements | |
| URL | https://github.com/openanalytics/daVis |
| Bug Reports | https://github.com/openanalytics/daVis/issues |
See More
| Suggests | AnnotationDbi, Biobase, ggrepel, ggtext, knitr, methods, org.Mm.eg.db, pander, plotly, rmarkdown, S4Vectors, scales, testthat, tools, BiocStyle |
| 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 | daVis_0.99.4.tar.gz |
| Windows Binary (x86_64) | daVis_0.99.4.zip |
| macOS Binary (big-sur-x86_64) | daVis_0.99.4.tgz |
| macOS Binary (sonoma-arm64) | daVis_0.99.4.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/daVis |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/daVis |
| Bioc Package Browser | https://code.bioconductor.org/browse/daVis/ |
| Package Short Url | https://bioconductor.org/packages/daVis/ |
| Package Downloads Report | Download Stats |