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This is the development version of eiR; for the stable release version, see eiR.

Accelerated similarity searching of small molecules

Bioconductor version: Development (3.19)

The eiR package provides utilities for accelerated structure similarity searching of very large small molecule data sets using an embedding and indexing approach.

Author: Kevin Horan, Yiqun Cao and Tyler Backman

Maintainer: Thomas Girke <thomas.girke at>

Citation (from within R, enter citation("eiR")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

eiR: Accelerated Similarity Searching of Small Molecules HTML R Script
Reference Manual PDF


biocViews BiomedicalInformatics, CellBasedAssays, Cheminformatics, Clustering, DataImport, Infrastructure, Metabolomics, MicrotitrePlateAssay, Pharmacogenetics, Pharmacogenomics, Proteomics, Software, Visualization
Version 1.43.0
In Bioconductor since BioC 2.12 (R-3.0) (11 years)
License Artistic-2.0
Depends R (>= 2.10.0), ChemmineR(>= 2.15.15), methods, DBI
Imports snow, tools, snowfall, RUnit, methods, ChemmineR, RCurl, digest, BiocGenerics, RcppAnnoy (>= 0.0.9)
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Suggests BiocStyle, knitcitations, knitr, knitrBootstrap, rmarkdown, RSQLite
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Follow Installation instructions to use this package in your R session.

Source Package eiR_1.43.0.tar.gz
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macOS Binary (x86_64) eiR_1.43.0.tgz
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