MSexplorer is an R/Shiny application for exploring microbiome analysis results from a multiple sclerosis study. It provides interactive views for differential abundance results, PCA, k-means clustering, 3D PCA, clinical association tests, survival analysis, and EDSS flow visualizations.
app.R,ui.R,server.R: Shiny application entry point and interface/server code.Functions.R: plotting, clustering, statistical testing, and helper functions.www/Data.Rds,www/metadata.Rds: derived data objects used by the app.www/home.png,www/loghi.png: images used by the app and displayed in this README.www/tables/001_bacteria_maaslin.tsv: differential abundance results displayed in the data explorer.
Install the required R packages:
install.packages(c(
"DT", "shinybusy", "shiny", "shinydashboard", "shinyjs", "plotly",
"ggplot2", "dplyr", "ggalluvial", "patchwork", "ggrepel",
"ggfortify", "ggforce", "factoextra", "tidyr", "purrr", "ggmosaic",
"clusterCrit", "concaveman", "survival", "survminer",
"RColorBrewer", "viridisLite"
))Start the application from the repository root:
shiny::runApp(".")Please cite the associated publication and this repository if you use MSexplorer. Update CITATION.cff with the final manuscript DOI and full author list before public release.
No software license has been selected yet. Add the license approved by the authors/institution before making the repository public or linking it from a publication.