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Cheminformatics Toolkit for R

Bioconductor version: Release (3.19)

ChemmineR is a cheminformatics package for analyzing drug-like small molecule data in R. Its latest version contains functions for efficient processing of large numbers of molecules, physicochemical/structural property predictions, structural similarity searching, classification and clustering of compound libraries with a wide spectrum of algorithms. In addition, it offers visualization functions for compound clustering results and chemical structures.

Author: Y. Eddie Cao, Kevin Horan, Tyler Backman, Thomas Girke

Maintainer: Thomas Girke <thomas.girke at>

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


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

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


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:

ChemmineR HTML R Script
Reference Manual PDF


biocViews BiomedicalInformatics, CellBasedAssays, Cheminformatics, Clustering, DataImport, Infrastructure, Metabolomics, MicrotitrePlateAssay, Pharmacogenetics, Pharmacogenomics, Proteomics, Software, Visualization
Version 3.56.0
In Bioconductor since BioC 2.3 (R-2.8) (15.5 years)
License Artistic-2.0
Depends R (>= 2.10.0), methods
Imports rjson, graphics, stats, RCurl, DBI, digest, BiocGenerics, Rcpp (>= 0.11.0), ggplot2, grid, gridExtra, png, base64enc, DT, rsvg, jsonlite, stringi
System Requirements GNU make
See More
Suggests RSQLite, scatterplot3d, gplots, fmcsR, snow, RPostgreSQL, BiocStyle, knitr, knitcitations, knitrBootstrap, ChemmineDrugs, png, rmarkdown, BiocManager, bibtex
Linking To Rcpp, BH
Enhances ChemmineOB
Depends On Me eiR, fmcsR, ChemmineDrugs
Imports Me bioassayR, CompoundDb, customCMPdb, eiR, fmcsR, MetID, chemodiv, DrugSim2DR, DRviaSPCN
Suggests Me ChemmineOB, xnet
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package ChemmineR_3.56.0.tar.gz
Windows Binary
macOS Binary (x86_64) ChemmineR_3.56.0.tgz
macOS Binary (arm64) ChemmineR_3.56.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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Package Short Url
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