# Run PathoStat

## 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 4.5.2 (2025-10-31)
    #> Platform: x86_64-pc-linux-gnu
    #> Running under: Ubuntu 24.04.3 LTS
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    #>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
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    #> [1] stats     graphics  grDevices utils     datasets  methods   base
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    #>  [9] buildtools_1.0.0 lifecycle_1.0.5  cli_3.6.5        sass_0.4.10
    #> [13] jquerylib_0.1.4  compiler_4.5.2   sys_3.4.3        tools_4.5.2
    #> [17] evaluate_1.0.5   bslib_0.10.0     yaml_2.3.12      otel_0.2.0
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