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 3.6.0 (2019-04-26)
#> 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_3.6.0 magrittr_1.5 htmltools_0.3.6 tools_3.6.0
#> [5] yaml_2.2.0 Rcpp_1.0.1 stringi_1.4.3 rmarkdown_1.12
#> [9] knitr_1.22 stringr_1.4.0 digest_0.6.18 xfun_0.6
#> [13] evaluate_0.13