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 (3.19)

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 (version "4.4") and enter:


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

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

BiocManager::install("omicplotR")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation


Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Bayesian, DNASeq, DifferentialExpression, GUI, GeneExpression, ImmunoOncology, Metagenomics, Microbiome, RNASeq, Sequencing, Software, Transcriptomics, Visualization
Version	1.23.0
In Bioconductor since	BioC 3.7 (R-3.5) (6 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
System Requirements
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Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
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