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 you want to install the latest development version of PathoStat from Github, use devtools to install it as follows:
#> R version 3.5.0 Patched (2018-05-03 r74699)
#> Platform: x86_64-w64-mingw32/x64 (64-bit)
#> Running under: Windows Server 2012 R2 x64 (build 9600)
#>
#> Matrix products: default
#>
#> locale:
#> [1] LC_COLLATE=C
#> [2] LC_CTYPE=English_United States.1252
#> [3] LC_MONETARY=English_United States.1252
#> [4] LC_NUMERIC=C
#> [5] LC_TIME=English_United States.1252
#>
#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
#>
#> loaded via a namespace (and not attached):
#> [1] compiler_3.5.0 backports_1.1.2 magrittr_1.5 rprojroot_1.3-2
#> [5] htmltools_0.3.6 tools_3.5.0 yaml_2.1.19 Rcpp_0.12.17
#> [9] stringi_1.2.2 rmarkdown_1.9 knitr_1.20 stringr_1.3.1
#> [13] digest_0.6.15 evaluate_0.10.1