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 3.6.1 (2019-07-05)
#> Platform: x86_64-apple-darwin15.6.0 (64-bit)
#> Running under: OS X El Capitan 10.11.6
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#> Matrix products: default
#> BLAS: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
#> LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
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#> locale:
#> [1] C/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
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#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
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#> loaded via a namespace (and not attached):
#> [1] compiler_3.6.1 magrittr_1.5 htmltools_0.4.0 tools_3.6.1
#> [5] yaml_2.2.0 Rcpp_1.0.2 stringi_1.4.3 rmarkdown_1.16
#> [9] knitr_1.25 stringr_1.4.0 digest_0.6.22 xfun_0.10
#> [13] rlang_0.4.1 evaluate_0.14