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 3.5.1 Patched (2018-07-12 r74967)
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#> Running under: OS X El Capitan 10.11.6
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#> [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_3.5.1 backports_1.1.2 magrittr_1.5 rprojroot_1.3-2
#> [5] htmltools_0.3.6 tools_3.5.1 yaml_2.2.0 Rcpp_1.0.0
#> [9] stringi_1.2.4 rmarkdown_1.10 knitr_1.20 stringr_1.3.1
#> [13] digest_0.6.18 evaluate_0.12