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 4.1.1 Patched (2021-08-22 r80813)
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#> Running under: macOS Mojave 10.14.6
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#> BLAS: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.0.dylib
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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] digest_0.6.28 R6_2.5.1 jsonlite_1.7.2 magrittr_2.0.1
#> [5] evaluate_0.14 rlang_0.4.12 stringi_1.7.5 jquerylib_0.1.4
#> [9] bslib_0.3.1 rmarkdown_2.11 tools_4.1.1 stringr_1.4.0
#> [13] xfun_0.27 yaml_2.2.1 fastmap_1.1.0 compiler_4.1.1
#> [17] htmltools_0.5.2 knitr_1.36 sass_0.4.0