Posts

Test

Hello world

Create R environments for teaching

In this post, I’ll describe a use of renv to manage a collection of environments for a training course, in a single Git repository. I will cover some caveats at the end of the post, so that you can decide whether this set up suits your own needs, but for now - before I give myself a chance to confuse you - I’ll just get straight into my process.

BiocPkgTools

Motivation There are currently 6,096 packages on Bioconductor, broken down as follows: Repository Packages data-annotation 2,693 data-experiment 855 software 2,516 workflows 32 In an effort to motivate myself to keep an eye out for interesting packages - both new and old - I have used the BiocPkgTools package to develop a website updated daily and feature packages selected randomly from each repository.

Making a map of COVID-19 cases

Overview I have added an interactive world map to my COVID-19 website using the leaflet package. Using my existing data preprocessing setup, it was incredibly easy to set up the interactive map!

Transiton from Travis CI to GitHub Actions

Overview The recent introduction of GitHub Actions makes a lot of our Travis CI build configurations redundant. In particular, the examples actions include: R-CMD-check using rcmdcheck::rcmdcheck() to check the package.

Writing my CV using pagedown

Wow! I have taken the time to write my CV using pagedown. And… WOW does it look beautiful! A single .Rmd file can simultaneously generate both an HTML and a PDF version.

Creating a dynamic Rmarkdown website for COVID-19 data

Overview This post refers to code available online as a GitHub repository. Create a new RStudio project Open the RStudio “New Project…” menu -> New Directory -> Simple R Markdown Website -> Type a folder name.

How to datapasta

I was recently told about datapasta, a jewel of a package that provides RStudio addins and functions to freely copy-paste data in and out of a source editor, formatted for immediate use.

iSEE workshop at Bioc2019!

The iSEE package will be presented as a workshop at the Bioconductor 2019 conference in New York City! What to expect Charlotte Soneson and I will be conducting a workshop that demonstrates the many features and usages of the iSEE package.