Run PathoStat

Solaiappan Manimaran, Yue Zhao

2024-05-01

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 4.4.0 beta (2024-04-15 r86425 ucrt)
#> Platform: x86_64-w64-mingw32/x64
#> 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_0.6.35     R6_2.5.1          fastmap_1.1.1     xfun_0.43        
#>  [5] cachem_1.0.8      knitr_1.46        htmltools_0.5.8.1 rmarkdown_2.26   
#>  [9] lifecycle_1.0.4   cli_3.6.2         sass_0.4.9        jquerylib_0.1.4  
#> [13] compiler_4.4.0    tools_4.4.0       evaluate_0.23     bslib_0.7.0      
#> [17] yaml_2.3.8        rlang_1.1.3       jsonlite_1.8.8