# Run PathoStat

#### Solaiappan Manimaran, Yue Zhao

#### 2019-10-29

## 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 3.6.1 (2019-07-05)
    #> Platform: x86_64-apple-darwin15.6.0 (64-bit)
    #> Running under: OS X El Capitan 10.11.6
    #>
    #> Matrix products: default
    #> BLAS:   /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
    #> LAPACK: /Library/Frameworks/R.framework/Versions/3.6/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] compiler_3.6.1  magrittr_1.5    htmltools_0.4.0 tools_3.6.1
    #>  [5] yaml_2.2.0      Rcpp_1.0.2      stringi_1.4.3   rmarkdown_1.16
    #>  [9] knitr_1.25      stringr_1.4.0   digest_0.6.22   xfun_0.10
    #> [13] rlang_0.4.1     evaluate_0.14