I've started exploring the Cheminformatics capabilities of Bioconductor, notably through the combination of the packages: ChemmineR, fmcsR, bioassayR and biomaRt. I am very interested in exploiting any publicly available drug-target activity assay databases e.g., PubChem, which is supported by the bioassayR package. In terms of activity assays, this is the extent of my knowledge. Is there additional support for activity assays besides PubChem within the Bioconductor software suite? My outcome would be to cluster drug/small molecules by their similar bioassay activity profiles.

Secondly, and of particular interest, is there an R/Bioconductor package to interface with the [clue.io] API? A had a little attempt a year back using Java, however, there is little point in reinventing the wheel if the capability exists.

A very useful resource for bioactivity data is ChEMBL. This includes many bioassays from PubChem but better curated. Their SQLite version here: ftp://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/latest/ can be easily accessed from within R (e.g using RSQLite). Detailed documentation on their database schema and table contents is available in the corresponding *.html file on the ftp page. For clue data you may want to take a look at the slinky package (https://bioconductor.org/packages/release/bioc/html/slinky.html).