Run PathoStat

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 4.4.2 (2024-10-31)
#> Platform: x86_64-pc-linux-gnu
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