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omicplotR

Visual Exploration of Omic Datasets Using a Shiny App


Bioconductor version: Release (3.18)

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 "4.3") and enter:


if (!require("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")
omicplotR: A tool for visualization of omic datasets as compositions HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Bayesian, DNASeq, DifferentialExpression, GUI, GeneExpression, ImmunoOncology, Metagenomics, Microbiome, RNASeq, Sequencing, Software, Transcriptomics, Visualization
Version 1.22.0
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
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Package Archives

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

Source Package omicplotR_1.22.0.tar.gz
Windows Binary omicplotR_1.22.0.zip
macOS Binary (x86_64) omicplotR_1.22.0.tgz
macOS Binary (arm64) omicplotR_1.22.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/omicplotR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/omicplotR
Bioc Package Browser https://code.bioconductor.org/browse/omicplotR/
Package Short Url https://bioconductor.org/packages/omicplotR/
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