How to identify R packages required for a variety of metanodes used in proteomics

Hi, I have been using a Knime-Docker platform to process proteomic data and so use several components reliant on Python and R, but which I hadnt had to worry about. However, as a remote user, the platform can be excruciatingly slow.
Recently, I have installed Knime 4.4 that allows me to rapidly perform many of the tasks locally. One of the drawbacks is the necessity of acquiring the packages for R required for several of the metanodes/components utilised (non-linear normalization, LIMMA, proDA, and several data visualisation metanodes).
So far, I have installed managed to install the R packages for LIMMA tests and Volcano plots. However, it is often unclear what packages are required. For example, the volcano plot required ggplot2 and ggrepel which I found out only from the error message in the knime console.
Is there any way to find out the package requirements of (often bespoke) metanodes before attempting to use them? Alternatively, is there a known repository of R packages packages used in 'omics data processing and visualisation?
Thanks for any feedback.

@0nly4phil at the beginning of every R code (or somewhere in the middle) there should be commands calling the packages like:


You could collect the and use them at the start. Another option once you have collected to packages would be to use conda and Python Conda Environment Propagation to store the packages needed so if you share the workflow they will be there.

As it happens I just published a story on Medium how to do that:

Many thanks. I shall read your earlier post now!

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