omXplore

This is the released version of omXplore; for the devel version, see omXplore.

Vizualization tools for 'omics' datasets with R

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DOI: 10.18129/B9.bioc.omXplore

Bioconductor version: Release (3.22)

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] ORCID iD ORCID: 0000-0002-5016-1203 , Thomas Burger [aut], Enora Fremy [ctb], Cyril Ariztegui [ctb]

Maintainer: Samuel Wieczorek <samuel.wieczorek at cea.fr>

Citation (from within R, enter citation("omXplore")):

Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
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 PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DataRepresentation, GUI, MassSpectrometry, QualityControl, ShinyApps, Software

Version 1.3.0

In Bioconductor since BioC 3.20 (R-4.4) (1 year)

License Artistic-2.0

Depends R (>= 4.4.0), methods

Imports DT, shiny, bs4Dash, waiter, thematic, MSnbase, PSMatch, SummarizedExperiment, MultiAssayExperiment, shinyBS, shinyjs, shinyjqui, RColorBrewer, gplots, highcharter, visNetwork, tibble, grDevices, stats, utils, htmlwidgets, vioplot, graphics, FactoMineR, dendextend, dplyr, factoextra, tidyr, nipals

System Requirements

URL https://github.com/prostarproteomics/omXplore https://prostarproteomics.github.io/omXplore/

Bug Reports https://github.com/prostarproteomics/omXplore/issues

Suggests knitr, rmarkdown, BiocStyle, testthat, Matrix, graph

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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package omXplore_1.3.0.tar.gz

Windows Binary (x86_64) omXplore_1.3.0.zip

macOS Binary (x86_64) omXplore_1.3.0.tgz

macOS Binary (arm64) omXplore_1.3.0.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/

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