Run PathoStat

Solaiappan Manimaran, Yue Zhao

2023-02-28

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:

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 4.2.2 (2022-10-31)
#> Platform: x86_64-apple-darwin17.0 (64-bit)
#> Running under: macOS Big Sur ... 10.16
#> 
#> Matrix products: default
#> BLAS:   /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
#> LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
#> 
#> locale:
#> [1] C/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> loaded via a namespace (and not attached):
#>  [1] digest_0.6.31   R6_2.5.1        jsonlite_1.8.4  evaluate_0.20  
#>  [5] rlang_1.0.6     cachem_1.0.7    cli_3.6.0       jquerylib_0.1.4
#>  [9] bslib_0.4.2     rmarkdown_2.20  tools_4.2.2     xfun_0.37      
#> [13] yaml_2.3.7      fastmap_1.1.1   compiler_4.2.2  htmltools_0.5.4
#> [17] knitr_1.42      sass_0.4.5