Tools based in R used in metabolomics

We have collected over time and collectively a large number of tools used in the field of metabolomics summarized via metaRbolomics Repository. Click on online book for access. This resource includes active code that is executed upon each build. The material, unless explicitly otherwise stated, is CC-BY 4.0 licenced.

Docker images

There is a docker image that contains the built environment to render the book at: https://hub.docker.com/repository/docker/sneumann/metarbolomics-book-base Output directory and output format are configurable via environment variables.

What is Docker? get started

Also check:

https://stackoverflow.com/questions/44143110/visualizing-r-function-dependencies

https://cran.r-project.org/web/packages/miniCRAN/vignettes/miniCRAN-dependency-graph.html

https://cran.r-project.org/web/packages/pkgnet/vignettes/pkgnet-intro.html pkgnet can analyze any R package locally installed. (Run installed.packages() to see the full list of packages installed on your system.)

An overview overview youtube presented by Steffen Neumann

Building the book

The travisScript.sh uses the Docker image and builds the book in the build directory.

Simply run

./travisScript.sh

to build the book. The output will be saved in the build/public directory.

docker pull sneumann/metarbolomics-book-base