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Bioconductor - omicplotR

omicplotR

This is the released version of omicplotR; for the devel version, see omicplotR.

Visual Exploration of Omic Datasets Using a Shiny App

Bioconductor version: Release (3.21)

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 "4.5") 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 1.28.0 In Bioconductor since BioC 3.7 (R-3.5) (7 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 URL See More Suggests Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives

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

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