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AntonelliLab / supersmartR

:eyeglasses::deciduous_tree: Towards a modular SUPERSMART pipeline in R
MIT License
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pplinR #10

Open DomBennett opened 6 years ago

DomBennett commented 6 years ago

I've been developing a common set of functions in R for running pipelines (cache'ing, parameters ...etc). Perhaps it would be best to pull of these things into a single package?

rvosa commented 6 years ago

Are there no generic tools or approaches for that?

I think that the user-friendly and development-friendly approach is to have loosely-coupled, compatible packages (so, the same objects, for example) and that users can mix and match them at will, or use other tools.

The way to pipeline that would be in an RMarkDown document, so that you get an "executable paper" where the whole procedure is run surrounded by prose description and with output graphics embedded (basically a supplementary methods section, but fully reproducible).