# Run PathoStat

#### Solaiappan Manimaran, Yue Zhao

#### 2025-03-05

## 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) (2025-03-02 r87868)
    #> Platform: aarch64-apple-darwin20
    #> Running under: macOS Ventura 13.7.1
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    #> BLAS:   /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib
    #> LAPACK: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0
    #>
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    #> [1] C/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
    #>
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    #> tzcode source: internal
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    #> [1] stats     graphics  grDevices utils     datasets  methods   base
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    #> loaded via a namespace (and not attached):
    #>  [1] digest_0.6.37     R6_2.6.1          fastmap_1.2.0     xfun_0.51
    #>  [5] cachem_1.1.0      knitr_1.49        htmltools_0.5.8.1 rmarkdown_2.29
    #>  [9] lifecycle_1.0.4   cli_3.6.4         sass_0.4.9        jquerylib_0.1.4
    #> [13] compiler_4.5.0    tools_4.5.0       evaluate_1.0.3    bslib_0.9.0
    #> [17] yaml_2.3.10       rlang_1.1.5       jsonlite_1.9.1