DOI: 10.18129/B9.bioc.omicplotR    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see omicplotR.

Visual Exploration of Omic Datasets Using a Shiny App

Bioconductor version: 3.12

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>

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biocViews Bayesian, DNASeq, DifferentialExpression, GUI, GeneExpression, ImmunoOncology, Metagenomics, Microbiome, RNASeq, Sequencing, Software, Transcriptomics, Visualization
Version 1.10.0
In Bioconductor since BioC 3.7 (R-3.5) (3 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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