Some Context A few months ago I applied to the Fellows Program of the Society of Molecular Biology and Evolution.

UpWhat Plot? Venn diagrams are commonly used to show the sizes of sets and their overlaps in an intuitive way. However, they can quickly become overly complicated when comparing more than a few sets. For this reason, the UpSet plot was developed as an alternative to Venn diagrams ( 1 ). I recently needed to create UpSet plots and looked for implementations in R, of which there are many.

I love microbiology. Bacteria in particular have fascinated me for a long time. If you can imagine some sort of biological function or behaviour, there is a bacterium somewhere that does it. ^{[ citation needed ]} There are parts of microbiology that I do not particularly enjoy though. (Micro)biological lab work can be time and resource intensive, particularly when both biological and technical replication are necessary.

This post is marks two special occasions. This is the first post I’m publishing on my personal website and the topic of the post is my first R package — tread. While tread has been out in the wild for a while now, this post sat around as an unfinished draft for far too long.