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Trying to get access to the Trinity R commands...

On the server I use it is not so easy to install the necessary R packages when using R --vanilla, so I can't run the Trinity perl scripts which uses R for differential gene expression and visualizations (basically everything described here). Anyone have access to the different RScripts files which are generated by Trinity?

Thanks,

Jon

trinity r rna-seq
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written by jon.brate jon.brate

Which Rscript do you need? Did you look at github? Here the R scripts for DE analysis.

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written by Benn Benn

Thanks, I found those, but I was actually looking for the R commands which are generated with the different perl scripts under the Differential Genexpression (I think a file called RScript is generated after running the perl script). These are no magic commands, but I am just interested in learning how to use DESeq2 to generate the different plots.

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written by jon.brate jon.brate

You can always install a local R via conda to have full control over your environment.

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written by ATpoint ATpoint

Thanks, I began installing a local copy of Trinity (on my Macbook), but I had problems compiling it so I stopped. Any experience installing Trinity locally?

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written by jon.brate jon.brate

With conda, there is no compilation. It is a package manager that takes full care of all dependencies, fetching pre-compiled binaries.

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written by ATpoint ATpoint

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