omicplotR

DOI: 10.18129/B9.bioc.omicplotR    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see omicplotR.

Visual Exploration of Omic Datasets Using a Shiny App

Bioconductor version: 3.13

A Shiny app for visual exploration of omic datasets as compositions, and differential abundance analysis using ALDEx2. Useful for exploring RNA-seq, meta-RNA-seq, 16s rRNA gene sequencing with visualizations such as principal component analysis biplots (coloured using metadata for visualizing each variable), dendrograms and stacked bar plots, and effect plots (ALDEx2). Input is a table of counts and metadata file (if metadata exists), with options to filter data by count or by metadata to remove low counts, or to visualize select samples according to selected metadata.

Author: Daniel Giguere [aut, cre], Jean Macklaim [aut], Greg Gloor [aut]

Maintainer: Daniel Giguere <dgiguer at uwo.ca>

Installation

To install this package, start R (version "4.1") and enter:

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

BiocManager::install("omicplotR")

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("omicplotR")

 

HTML	R Script	omicplotR: A tool for visualization of omic datasets as compositions
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Bayesian, DNASeq, DifferentialExpression, GUI, GeneExpression, ImmunoOncology, Metagenomics, Microbiome, RNASeq, Sequencing, Software, Transcriptomics, Visualization
Version	1.12.0
In Bioconductor since	BioC 3.7 (R-3.5) (3.5 years)
License	MIT + file LICENSE
Depends	R (>= 3.6), ALDEx2(>= 1.18.0)
Imports	compositions, DT, grDevices, knitr, jsonlite, matrixStats, rmarkdown, shiny, stats, vegan, zCompositions
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Package Archives

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

Source Package	omicplotR_1.12.0.tar.gz
Windows Binary	omicplotR_1.12.0.zip
macOS 10.13 (High Sierra)	omicplotR_1.12.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/omicplotR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/omicplotR
Package Short Url	https://bioconductor.org/packages/omicplotR/
Package Downloads Report	Download Stats