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I'm using RStudio notebooks heavily in my latest bioinformatics analysis pipeline. They're a great way to produce an HTML report containing code, exposition, re
by rcthompson 9y ago
I'm using RStudio notebooks heavily in my latest bioinformatics analysis pipeline. They're a great way to produce an HTML report containing code, exposition, results, and plots all in one place.
https://github.com/DarwinAwardWinner/CD4-csaw https://github.com/DarwinAwardWinner/CD4-csaw (look at scripts/*.Rmd)
- alexilliamson 9y agoThanks for sharing... I'm always excited to see examples of RStudio notebooks in the wild.
- minimaxir 9y agoI wrote an article a few months ago on the differences between R Notebooks and Jupyter Notebooks (and why, IMO, R Notebooks are better): http://minimaxir.com/2017/06/r-notebooks/ http://minimaxir.com/2017/06/r-notebooks/
- peatmoss 9y agoYup, revision control is the elephant in the room with Jupyter, and why I struggle to recommend it for reproducible research. R Notebooks followed the org-mode model of keeping a simple, revisionable document with code interspersed.
- extr 9y agoR notebooks are the bees knees and frankly I'm surprised Jupyter hasn't borrowed more from them. It's so much easier being in plain-text until render time, and the output is easier to manage because you can trivially decide what chunks you want to echo, evaluate, plot at 2x size...etc without any change to the interactive usage. Not to mention you get to retain your nice IDE features like good code-completion, doc lookup, version control... I am excited for Jupyter Lab and it's a step in the right direction. But it feels a little bit like they're reinventing the wheel with some of this stuff. I would gladly pay money for a python copy of the R ecosystem with RStudio, R markdown, R notebooks, where everything just works great by default.