# Run PathoStat

#### Solaiappan Manimaran, Yue Zhao

#### 2022-11-01

## 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 4.2.1 (2022-06-23 ucrt)
    #> Platform: x86_64-w64-mingw32/x64 (64-bit)
    #> Running under: Windows Server x64 (build 20348)
    #>
    #> Matrix products: default
    #>
    #> locale:
    #> [1] LC_COLLATE=C
    #> [2] LC_CTYPE=English_United States.utf8
    #> [3] LC_MONETARY=English_United States.utf8
    #> [4] LC_NUMERIC=C
    #> [5] LC_TIME=English_United States.utf8
    #>
    #> attached base packages:
    #> [1] stats     graphics  grDevices utils     datasets  methods   base
    #>
    #> loaded via a namespace (and not attached):
    #>  [1] digest_0.6.30   R6_2.5.1        jsonlite_1.8.3  magrittr_2.0.3
    #>  [5] evaluate_0.17   stringi_1.7.8   rlang_1.0.6     cachem_1.0.6
    #>  [9] cli_3.4.1       jquerylib_0.1.4 bslib_0.4.0     rmarkdown_2.17
    #> [13] tools_4.2.1     stringr_1.4.1   xfun_0.34       yaml_2.3.6
    #> [17] fastmap_1.1.0   compiler_4.2.1  htmltools_0.5.3 knitr_1.40
    #> [21] sass_0.4.2