Run PathoStat

Solaiappan Manimaran, Yue Zhao

2023-04-26

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 4.3.0 RC (2023-04-13 r84269 ucrt)
#> Platform: x86_64-w64-mingw32/x64 (64-bit)
#> Running under: Windows Server 2022 x64 (build 20348)
#> 
#> Matrix products: default
#> 
#> 
#> locale:
#> [1] LC_COLLATE=C                          
#> [2] LC_CTYPE=English_United States.utf8   
#> [3] LC_MONETARY=English_United States.utf8
#> [4] LC_NUMERIC=C                          
#> [5] LC_TIME=English_United States.utf8    
#> 
#> time zone: America/New_York
#> tzcode source: internal
#> 
#> 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        fastmap_1.1.1   xfun_0.39      
#>  [5] cachem_1.0.7    knitr_1.42      htmltools_0.5.5 rmarkdown_2.21 
#>  [9] cli_3.6.1       sass_0.4.5      jquerylib_0.1.4 compiler_4.3.0 
#> [13] tools_4.3.0     evaluate_0.20   bslib_0.4.2     yaml_2.3.7     
#> [17] rlang_1.1.0     jsonlite_1.8.4