I’ve been working on some RNAi projects and part of that involved generating descriptors for sequences. It turns out that the Biostrings package is very handy and high performance. So, our database contains a catalog for an siRNA library with ~ 27,000 target DNA sequences. To get at the siRNA sequence, we need to convert […]
New Versions of rcdk and rcdklibs
I’ve put released an update to rcdk and rcdklibs on CRAN – right now source packages are available, but binary ones should show up soon. Both packages should be updated together. These packages integrate the CDK into the R environment and simplifies a number of cheminformatics tasks. These versions used CDK 1.3.6 and JCP 16, […]
A Quick Look at the GSK Malaria Dataset
A few days ago, GSK released an approximately 13,000 member compound library (using the CC0 license) that had been tested for activity against P. falciparum. The structures and data have been deposited into ChEMBL and a paper is available, that describes the screening project and results. Following this announcement there was a thread on FriendFeed, where […]
New Version of rcdk
Based on feedback from the recent R workshop at the EBI, I’ve updated the rcdk package to include more methods operating on atoms, a modification to parse.smiles to allow it to handle a vector of SMILES strings, which makes it more R-like (thanks to Tobias Verbeke for the patch). In addition, one can now load […]
Spreading the Word About R & Cheminformatics
These last few days I’ve been in the UK for an EBI workshop on cheminformatics in R. It was a two day workshop, the first day focusing on general cheminormatics in R using the rcdk and rpubchem packages, and the second day focusing on doing mass spectrometry in R using XCMS and Rdisop, run by […]