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 4.2.0 RC (2022-04-19 r82224)
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#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
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#> [1] digest_0.6.29 R6_2.5.1 jsonlite_1.8.0 magrittr_2.0.3
#> [5] evaluate_0.15 stringi_1.7.6 rlang_1.0.2 cli_3.3.0
#> [9] jquerylib_0.1.4 bslib_0.3.1 rmarkdown_2.14 tools_4.2.0
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#> [17] compiler_4.2.0 htmltools_0.5.2 knitr_1.38 sass_0.4.1