Run PathoStat

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:

  • Data Summary and Filtering
  • Relative Abundance plots (Stacked Bar Plot, Heatmap)
  • Multiple species boxplot visualization
  • Diversity analysis (Alpha and Beta diversity)
  • Differential Expression (DEseq2, edgeR)
  • Dimension Reduction (PCA, PCoA)
  • Biomarker identification

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 4.4.1 (2024-06-14)
#> Platform: x86_64-pc-linux-gnu
#> Running under: Ubuntu 24.04.1 LTS
#> 
#> Matrix products: default
#> BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
#> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so;  LAPACK version 3.12.0
#> 
#> locale:
#>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
#>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=C              
#>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
#>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
#>  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
#> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
#> 
#> time zone: Etc/UTC
#> tzcode source: system (glibc)
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#> [1] rmarkdown_2.28
#> 
#> loaded via a namespace (and not attached):
#>  [1] digest_0.6.37     R6_2.5.1          fastmap_1.2.0     xfun_0.48        
#>  [5] maketools_1.3.1   cachem_1.1.0      knitr_1.48        htmltools_0.5.8.1
#>  [9] buildtools_1.0.0  lifecycle_1.0.4   cli_3.6.3         sass_0.4.9       
#> [13] jquerylib_0.1.4   compiler_4.4.1    sys_3.4.3         tools_4.4.1      
#> [17] evaluate_1.0.1    bslib_0.8.0       yaml_2.3.10       jsonlite_1.8.9   
#> [21] rlang_1.1.4