# Run PathoStat

#### Solaiappan Manimaran, Yue Zhao

#### 2021-05-19

## 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 4.1.0 RC (2021-05-10 r80283)
    #> Platform: x86_64-apple-darwin17.0 (64-bit)
    #> Running under: macOS Mojave 10.14.6
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    #> Matrix products: default
    #> BLAS:   /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.dylib
    #> LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
    #>
    #> locale:
    #> [1] C/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
    #>
    #> attached base packages:
    #> [1] stats     graphics  grDevices utils     datasets  methods   base
    #>
    #> loaded via a namespace (and not attached):
    #>  [1] digest_0.6.27     R6_2.5.0          jsonlite_1.7.2    magrittr_2.0.1
    #>  [5] evaluate_0.14     rlang_0.4.11      stringi_1.6.2     jquerylib_0.1.4
    #>  [9] bslib_0.2.5.1     rmarkdown_2.8     tools_4.1.0       stringr_1.4.0
    #> [13] xfun_0.23         yaml_2.2.1        compiler_4.1.0    htmltools_0.5.1.1
    #> [17] knitr_1.33        sass_0.4.0