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What are the user friendly R packages available for analyzing shotgun proteomics data?

Has anyone had an experience in analyzing shotgun mass spectrometry data (unlabelled) Q-TOF uding R programming?

What are the user-friendly packages with examples?

r proteomics mass spectrometry
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written by WUSCHEL WUSCHEL

Please define user-friendly.

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written by Benn Benn

with having access to real-world examples/explanations!

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written by WUSCHEL WUSCHEL

What have your tried? RforProteomics? From where do you want to use R? From RAW data?

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written by Benn Benn

Thanks for trying to help Nota. I have not tried anything yet. Yes from the raw data. (.d files)

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written by WUSCHEL WUSCHEL

I haven't found an R package yet that can start from .RAW files, but there is a linux command line version of MaxQuant available now.

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written by Benn Benn

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