# Run PathoStat

#### Solaiappan Manimaran, Yue Zhao

#### 2018-06-02

## 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.

    source("http://bioconductor.org/biocLite.R")
    biocLite("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 3.5.0 Patched (2018-05-03 r74699)
    #> Platform: x86_64-w64-mingw32/x64 (64-bit)
    #> Running under: Windows Server 2012 R2 x64 (build 9600)
    #>
    #> Matrix products: default
    #>
    #> locale:
    #> [1] LC_COLLATE=C
    #> [2] LC_CTYPE=English_United States.1252
    #> [3] LC_MONETARY=English_United States.1252
    #> [4] LC_NUMERIC=C
    #> [5] LC_TIME=English_United States.1252
    #>
    #> attached base packages:
    #> [1] stats     graphics  grDevices utils     datasets  methods   base
    #>
    #> loaded via a namespace (and not attached):
    #>  [1] compiler_3.5.0  backports_1.1.2 magrittr_1.5    rprojroot_1.3-2
    #>  [5] htmltools_0.3.6 tools_3.5.0     yaml_2.1.19     Rcpp_0.12.17
    #>  [9] stringi_1.2.2   rmarkdown_1.9   knitr_1.20      stringr_1.3.1
    #> [13] digest_0.6.15   evaluate_0.10.1