omicsViewer

DOI: 10.18129/B9.bioc.omicsViewer    

This is the development version of omicsViewer; for the stable release version, see omicsViewer.

Interactive and explorative visualization of SummarizedExperssionSet or ExpressionSet using omicsViewer

Bioconductor version: Development (3.16)

omicsViewer visualizes ExpressionSet (or SummarizedExperiment) in an interactive way. The omicsViewer has a separate back- and front-end. In the back-end, users need to prepare an ExpressionSet that contains all the necessary information for the downstream data interpretation. Some extra requirements on the headers of phenotype data or feature data are imposed so that the provided information can be clearly recognized by the front-end, at the same time, keep a minimum modification on the existing ExpressionSet object. The pure dependency on R/Bioconductor guarantees maximum flexibility in the statistical analysis in the back-end. Once the ExpressionSet is prepared, it can be visualized using the front-end, implemented by shiny and plotly. Both features and samples could be selected from (data) tables or graphs (scatter plot/heatmap). Different types of analyses, such as enrichment analysis (using Bioconductor package fgsea or fisher's exact test) and STRING network analysis, will be performed on the fly and the results are visualized simultaneously. When a subset of samples and a phenotype variable is selected, a significance test on means (t-test or ranked based test; when phenotype variable is quantitative) or test of independence (chi-square or fisher’s exact test; when phenotype data is categorical) will be performed to test the association between the phenotype of interest with the selected samples. Additionally, other analyses can be easily added as extra shiny modules. Therefore, omicsViewer will greatly facilitate data exploration, many different hypotheses can be explored in a short time without the need for knowledge of R. In addition, the resulting data could be easily shared using a shiny server. Otherwise, a standalone version of omicsViewer together with designated omics data could be easily created by integrating it with portable R, which can be shared with collaborators or submitted as supplementary data together with a manuscript.

Author: Chen Meng [aut, cre]

Maintainer: Chen Meng <mengchen18 at gmail.com>

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

Installation

To install this package, start R (version "4.2") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("omicsViewer")

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("omicsViewer")

 

HTML R Script quickStart.html
PDF   Reference Manual
Text   NEWS
Video   01 Introduction to the input data

Details

biocViews DifferentialExpression, GeneSetEnrichment, MotifDiscovery, Network, NetworkEnrichment, Software, Visualization
Version 1.1.3
In Bioconductor since BioC 3.15 (R-4.2) (< 6 months)
License GPL-2
Depends R (>= 4.2)
Imports survminer, survival, fastmatch, reshape2, stringr, beeswarm, grDevices, DT, shiny, shinythemes, shinyWidgets, plotly, networkD3, httr, matrixStats, RColorBrewer, Biobase, fgsea, openxlsx, psych, shinybusy, ggseqlogo, htmlwidgets, graphics, grid, stats, utils, methods, shinyjs, curl, flatxml, ggplot2, S4Vectors, SummarizedExperiment, RSQLite, Matrix, shinycssloaders
LinkingTo
Suggests BiocStyle, knitr, rmarkdown, unittest
SystemRequirements
Enhances
URL https://github.com/mengchen18/omicsViewer
BugReports https://github.com/mengchen18/omicsViewer
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package omicsViewer_1.1.3.tar.gz
Windows Binary omicsViewer_1.1.3.zip
macOS 10.13 (High Sierra) omicsViewer_1.1.3.tgz
Source Repository git clone https://git.bioconductor.org/packages/omicsViewer
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/omicsViewer
Package Short Url https://bioconductor.org/packages/omicsViewer/
Package Downloads Report Download Stats

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