omicplotR
Visual Exploration of Omic Datasets Using a Shiny App
Bioconductor version: 3.23 · Package version: 1.32.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("omicplotR")Details
| Maintainer | Daniel Giguere <dgiguer@uwo.ca> |
| Author | Daniel Giguere [aut, cre], Jean Macklaim [aut], Greg Gloor [aut] |
| License | MIT + file LICENSE |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Bayesian, DNASeq, DifferentialExpression, GUI, GeneExpression, ImmunoOncology, Metagenomics, Microbiome, RNASeq, Sequencing, Software, Transcriptomics, Visualization |
| Package Short Url | https://bioconductor.org/packages/omicplotR/ |
Citation
From within R, enter citation("omicplotR"):
Daniel Giguere, Jean Macklaim, Greg Gloor. omicplotR: Visual Exploration of Omic Datasets Using a Shiny App. doi:10.18129/B9.bioc.omicplotR, R package version 1.32.0, https://bioconductor.org/packages/omicplotR.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | omicplotR_1.32.0.tar.gz |
| Windows binary (x86_64) | omicplotR_1.32.0.zip |
| macOS binary (arm64) | omicplotR_1.32.0.tgz |
| macOS binary (x86_64) | omicplotR_1.32.0.tgz |
Dependencies
Depends: R (>= 3.6), ALDEx2 (>= 1.18.0)
Imports: compositions, DT, grDevices, knitr, jsonlite, matrixStats, rmarkdown, shiny, stats, vegan, zCompositions