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:
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:
#> 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