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 4.2.2 (2022-10-31)
#> Platform: aarch64-apple-darwin20 (64-bit)
#> Running under: macOS Ventura 13.0
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#> BLAS: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
#> LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/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] digest_0.6.31 R6_2.5.1 lifecycle_1.0.3 jsonlite_1.8.4
#> [5] magrittr_2.0.3 evaluate_0.20 stringi_1.7.12 rlang_1.0.6
#> [9] cachem_1.0.6 cli_3.6.0 jquerylib_0.1.4 bslib_0.4.2
#> [13] vctrs_0.5.1 rmarkdown_2.20 tools_4.2.2 stringr_1.5.0
#> [17] glue_1.6.2 xfun_0.36 yaml_2.3.6 fastmap_1.1.0
#> [21] compiler_4.2.2 htmltools_0.5.4 knitr_1.41 sass_0.4.4