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 4.3.1 (2023-06-16 ucrt)
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#> Running under: Windows Server 2022 x64 (build 20348)
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#> time zone: America/New_York
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#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
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#> [1] digest_0.6.33 R6_2.5.1 fastmap_1.1.1 xfun_0.40
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#> [9] cli_3.6.1 sass_0.4.7 jquerylib_0.1.4 compiler_4.3.1
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#> [17] rlang_1.1.1 jsonlite_1.8.7