There are a variety of pathway databases such as KEGG, Reactome and Wikipathways. One of my projects involves pathway analysis, and it’d be nice to easily display them. In many cases, one can simply display a pre-generated image of the pathway (such as in KEGG), but in general, interactivity is nice. However, the latter would […]
Plate Well Series Plots in R
Plate well series plots are a common way to summarize well level data across multiple plates in a high throughput screen. An example can be seen in Zhang et al. As I’ve been working with RNAi screens, this visualization has been a useful way to summarize screening data and the various transformations on that data. […]
From Theory to Practice
Some time back, John Van Drie and myself had done some work on characterizing structure-activity cliffs, which are molecules that have very similar structures but very different activities. The term originated from Maggiora, who suggested that this was a reason for the failure of many QSAR models. At the same time, such cliffs can represent […]
Hit Selection Methods for RNAi Screens
Over the last few weeks I’ve been getting up to speed on RNAi screening (see Lord et al for a nice overview) and one of the key features in this approach is to reliably select hits for followup. In many ways it is similar to hit selection in small molecule HTS but also employs techniques […]
R and Oracle
It’s been a while since my last post, but I’m getting up to speed at work. It’s been less than a month, but there’s already a ton of cool stuff going on. One of the first things I’ve been getting to grips with is the data infrastructure at the NCGC, which is based around Oracle. […]