PathoStat: Statistical Microbiome Analysis Toolkit

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:

1. Data Summary and Filtering 
2. Relative Abundance plots (Stacked Bar Plot, Heatmap)
3. Multiple species boxplot visualization
4. Diversity analysis (Alpha and Beta diversity)
5. Differential Expression (DEseq2, edgeR)
6. Dimension Reduction (PCA, PCoA)
7. Biomarker identification

runPathoStat is the pipeline function that generates the PathoStat report and launches shiny app when in interactive mode. It combines all the functions into one step.

Run Pathostat

To launch PathoStat in R, just enter the command:

runPathoStat()

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("compbiomed/PathoStat")

If all went well you should now be able to load PathoStat:

require(PathoStat)
vignette('PathoStat-vignette', package='PathoStat')
runPathoStat()