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.
To launch PathoStat in R, just enter the command:
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:
If all went well you should now be able to load PathoStat:
require(PathoStat) vignette('PathoStat-vignette', package='PathoStat') runPathoStat()
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.