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 version 4.6.0 RC (2026-04-17 r89917)
#> Platform: x86_64-pc-linux-gnu
#> Running under: Ubuntu 24.04.4 LTS
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#> Matrix products: default
#> BLAS:   /home/biocbuild/bbs-3.24-bioc/R/lib/libRblas.so 
#> LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0  LAPACK version 3.12.0
#> 
#> locale:
#>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
#>  [3] LC_TIME=en_GB              LC_COLLATE=C              
#>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
#>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
#>  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
#> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
#> 
#> time zone: America/New_York
#> tzcode source: system (glibc)
#> 
#> 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_0.57      
#>  [5] cachem_1.1.0    knitr_1.51      htmltools_0.5.9 rmarkdown_2.31 
#>  [9] lifecycle_1.0.5 cli_3.6.6       sass_0.4.10     jquerylib_0.1.4
#> [13] compiler_4.6.0  tools_4.6.0     evaluate_1.0.5  bslib_0.10.0   
#> [17] yaml_2.3.12     otel_0.2.0      rlang_1.2.0     jsonlite_2.0.0