Thornton Lab policies and protocols

Lab manual for the Thornton lab at UC Irvine

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Working remotely
Note taking, lab notebooks, etc..
Content generation with R Markdown
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Text editors for coding
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Thornton lab main page

Tools for generating reports

Recommendation

KT strongly recommends using R markdown over Jupyter notebooks.

Rationale

The main reasons for this recommendation are:

But Jupyter is fine, too!

As always, there are exceptions to this rule! KT likes Jupyter notebooks, and they are the best/only game in town for generating interactive Python graphics.

R Markdown (and R Studio)

R Markdown is a “flavor” of markdown. The way most people use R markdown is within RStudio. Rstudio is an “integrated development environment”, or IDE for the R programming language. It differs from “vanilla” markdown is that you can execute R code display graphics generated via R. With the reticulate package installed, you may also do the same with Python code.

More info on R markdown can be found in the section Generating content with R markdown on the main page.

Pros

Cons

Jupyter Lab

Jupyter lab is a browser-based notebook application that supports many different languages, including R and Python. Its language agnosticism means that it is not an IDE for any language. Rather, it is a nice application for entering text and code and making reports, slides, etc..

Pros

Cons