Version 1.4.3 of rpubchem is out on CRAN. There’s some minor code cleanups and also a new function called get.aid.by.cid which allows you to get assay ID’s based on whether they contain a compound (either as an active, inactive, discrepant or just tested). This uses PUG to perform the query, so can be a bit […]
Frequency of a Term via PubMed
A little while back, Egon posted a question on FriendFeed, asking whether there was an easy way, preferably a service, to determine and plot the usage count of a term in PubMed by year. This is simple enough using the Entrez Utilities CGI. A quick Python script to do this (with minimal error checking) is […]
Updated Versions of R Packages
New versions of several of my R packages are now available on CRAN. rcdk 2.9.6 goes along with rcdklibs 1.2.3. The latter now uses the most recent cdk-1.2.x branch from Github. The former fixes a number of bugs relating to descriptor calculations, saving molecules in SD format and setting/getting properties on molecules. Unfortunately, because the […]
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. […]
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. […]