omicplotR

DOI: 10.18129/B9.bioc.omicplotR    

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

Visual Exploration of Omic Datasets Using a Shiny App

Bioconductor version: Development (3.8)

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>

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

Installation

To install this package, start R and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("omicplotR", version = "devel")

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, Metagenomics, Microbiome, RNASeq, Sequencing, Software, Transcriptomics, Visualization
Version 1.1.4
License MIT + file LICENSE
Depends R (>= 3.5)
Imports ALDEx2(>= 1.8.0), compositions, grDevices, knitr, matrixStats, rmarkdown, shiny, stats, vegan, zCompositions
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Build Report  

Package Archives

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

Source Package omicplotR_1.1.4.tar.gz
Windows Binary omicplotR_1.1.4.zip
Mac OS X 10.11 (El Capitan) omicplotR_1.1.4.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 http://bioconductor.org/packages/omicplotR/
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