omXplore
This is the development version of omXplore; for the stable release version, see omXplore.
Vizualization tools for 'omics' datasets with R
Bioconductor version: Development (3.24)
This package contains a collection of functions (written as shiny modules) for the visualisation and the statistical analysis of omics data. These plots can be displayed individually or embedded in a global Shiny module. Additionaly, it is possible to integrate third party modules to the main interface of the package omXplore.
Author: Samuel Wieczorek [aut, cre]
, Thomas Burger [aut], Enora Fremy [ctb], Cyril Ariztegui [ctb], Manon Gaudin [ctb]
Maintainer: Samuel Wieczorek <samuel.wieczorek at cea.fr>
citation("omXplore")):
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("omXplore")
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("omXplore")| Adding third party plots | HTML | R Script |
| omXplore | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DataRepresentation, GUI, MassSpectrometry, QualityControl, ShinyApps, Software |
| Version | 1.7.0 |
| In Bioconductor since | BioC 3.20 (R-4.4) (2 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.5.0), methods |
| Imports | DT, shiny, MSnbase, PSMatch, SummarizedExperiment, MultiAssayExperiment, shinyBS, shinyjs, shinyjqui, RColorBrewer, gplots, plotly, visNetwork, tibble, grDevices, stats, utils, htmlwidgets, vioplot, graphics, FactoMineR, dendextend, dplyr, factoextra, tidyr, nipals, Biobase |
| System Requirements | |
| URL | https://github.com/edyp-lab/omXplore https://edyp-lab.github.io/omXplore/ |
| Bug Reports | https://github.com/edyp-lab/omXplore/issues |
See More
| Suggests | knitr, rmarkdown, BiocStyle, testthat, Matrix, graph |
| 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 | omXplore_1.7.0.tar.gz |
| Windows Binary (x86_64) | omXplore_1.7.0.zip |
| macOS Binary (big-sur-x86_64) | omXplore_1.7.0.tgz |
| macOS Binary (sonoma-arm64) | omXplore_1.7.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/omXplore |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/omXplore |
| Bioc Package Browser | https://code.bioconductor.org/browse/omXplore/ |
| Package Short Url | https://bioconductor.org/packages/omXplore/ |
| Package Downloads Report | Download Stats |