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
8. Pathway analysis

Run Pathostat

To launch PathoStat in R, just enter the command:

runPathoStat()

Installation

Use devtools to install it as follows:

require(devtools)
install_github("jasonzhao0307/PathoStat")

Troubleshooting with Installation

If you are having issues with the installation, you may have to setup local directory, if you do not have permissions to install in the default location for R. You may also want to load a version of R 3.3.1 or higher.

export R_LIBS="/my_own_local_directory/R_libs"
module load R/R-3.2.4

And do something like the following

install.packages("devtools", repos="http://cran.r-project.org", 
    lib="/my_own_local_directory/R_libs")