omicplotR
Visual Exploration of Omic Datasets Using a Shiny App
Bioconductor version: Release (3.20)
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("omicplotR")):
Installation
To install this package, start R (version "4.4") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Bayesian, DNASeq, DifferentialExpression, GUI, GeneExpression, ImmunoOncology, Metagenomics, Microbiome, RNASeq, Sequencing, Software, Transcriptomics, Visualization |
| Version | 1.26.0 |
| In Bioconductor since | BioC 3.7 (R-3.5) (6.5 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.
| Source Package | omicplotR_1.26.0.tar.gz |
| Windows Binary (x86_64) | omicplotR_1.26.0.zip |
| macOS Binary (x86_64) | omicplotR_1.26.0.tgz |
| macOS Binary (arm64) | omicplotR_1.26.0.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/ |
| Package Downloads Report | Download Stats |