The eiR package provides utilities for accelerated structure similarity searching of very large small molecule data sets using an embedding and indexing approach. eiR is hosted on [Bioconductor](http://www.bioconductor.org) where you can find the [Release](http://www.bioconductor.org/packages/2.14/bioc/html/eiR.html) version and the [Development](http://www.bioconductor.org/packages/devel/bioc/html/eiR.html) version.