Run PathoStat

In PathoStat: PathoStat Statistical Microbiome Analysis Package

knitr::opts_chunk$set(
    collapse = TRUE,
    comment = "#>"
)

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

sessionInfo()

PathoStat documentation built on Nov. 8, 2020, 5:28 p.m.