The PlasmoGenEpi R-universe

The package ecosystem simplifying tool installation

The rOpenSci R-universe system provides a framework for users and developers of R-packages to create a package ‘ecosystem’ in a simple and accessible way. The R-universe build infrastructure provides a high-performance package server, integrated monitoring tools, and REST APIs, including a front-end dashboard, to provide a dynamics and automated R package repository.

rOpenSci R-universe logo

This infrastructure provides pre-built packages, which greatly simplifies installation of non-CRAN packages and those with complex dependencies such as C++ compilers. The R-universe platform is used by professionals from different industries including brain research, climate change, infectious disease research and government data analysis. If you are interested in learning more about the R-universe infrastructure, you can check out this blog post and we encourage you to explore the resources at the rOpenSci R-universe website and the R-universe dashboard.

The plasmogenepi.r-universe

The PlasmoGenEpi community has created a dedicated plasmogenepi.r-universe with R packages relevant to Plasmodium genomic analyses.

The dashboard build page can be seen below, where a timeline of updates to the packages is displayed as a bar chart, and below it the general information for each package, including links to the Github repository, who is the main maintaner of the package, and when it was last built.

The PlasmoGenEpi R-universe build dashboard

You can navigate through to the ‘Packages’ tab for more detailed descriptions of each package, as seen below.

The PlasmoGenEpi R-universe package dashboard

You can navigate through to the ‘API’ tab for more details on how to access the r-universe via its API, as seen below.

The PlasmoGenEpi R-universe package dashboard

Installation instructions

Having R packages within the R-universe ecosystem makes the installation process much simpler! This is an important aim of our community to ensure that the R packages available for analysis of Plasmodium genomic analysis are easily accessible to end-users.

Below we show an example of how you could install the DRpower package via the plasmogenepi.r-universe.

You can see how easy this will be with one line of code! 🙌
# Install 'DRpower' in R:
install.packages('DRpower', 
                 repos = c('https://plasmogenepi.r-universe.dev', 
                           'https://cloud.r-project.org'))

All the tool tutorials in PGEforge have installation instructions, and where applicable, provide instructions for installation via the plasmogenepi.r-universe.

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