Run PathoStat

Solaiappan Manimaran, Yue Zhao

2021-10-26

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 4.1.1 Patched (2021-08-22 r80813)
#> Platform: x86_64-apple-darwin17.0 (64-bit)
#> Running under: macOS Mojave 10.14.6
#> 
#> Matrix products: default
#> BLAS:   /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.0.dylib
#> LAPACK: /Library/Frameworks/R.framework/Versions/4.1/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_0.6.28   R6_2.5.1        jsonlite_1.7.2  magrittr_2.0.1 
#>  [5] evaluate_0.14   rlang_0.4.12    stringi_1.7.5   jquerylib_0.1.4
#>  [9] bslib_0.3.1     rmarkdown_2.11  tools_4.1.1     stringr_1.4.0  
#> [13] xfun_0.27       yaml_2.2.1      fastmap_1.1.0   compiler_4.1.1 
#> [17] htmltools_0.5.2 knitr_1.36      sass_0.4.0