Introduction

PathoStat is a R shiny package, designed for performing Statistical Microbiome Analysis on metagenomics results from sequencing data samples. In particular, it supports analyses on the PathoScope generated report files.

The package includes:

• Data Summary and Filtering
• Relative Abundance plots (Stacked Bar Plot, Heatmap)
• Multiple species boxplot visualization
• Diversity analysis (Alpha and Beta diversity)
• Differential Expression (DEseq2, edgeR)
• Dimension Reduction (PCA, PCoA)
• Biomarker identification

Installation

To begin, install Bioconductor and simply run the following to automatically install PathoStat and all the dependencies as follows.

if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install("PathoStat")

If you want to install the latest development version of PathoStat from Github, use devtools to install it as follows:

require(devtools)
install_github("mani2012/PathoStat", build_vignettes=TRUE)

Run Pathostat

require(PathoStat)
runPathoStat()

Session info

#> R Under development (unstable) (2025-11-04 r88984)
#> Platform: aarch64-apple-darwin20
#> Running under: macOS Ventura 13.7.8
#> 
#> Matrix products: default
#> BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
#> LAPACK: /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.1
#> 
#> locale:
#> [1] C/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
#> 
#> time zone: America/New_York
#> tzcode source: internal
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> loaded via a namespace (and not attached):
#>  [1] digest_0.6.39   R6_2.6.1        fastmap_1.2.0   xfun_0.54      
#>  [5] cachem_1.1.0    knitr_1.50      htmltools_0.5.9 rmarkdown_2.30 
#>  [9] lifecycle_1.0.4 cli_3.6.5       sass_0.4.10     jquerylib_0.1.4
#> [13] compiler_4.6.0  tools_4.6.0     evaluate_1.0.5  bslib_0.9.0    
#> [17] yaml_2.3.11     rlang_1.1.6     jsonlite_2.0.0