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This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

R Interface with InterMine-Powered Databases

Bioconductor version: Release (3.19)

Databases based on the InterMine platform such as FlyMine, modMine (modENCODE), RatMine, YeastMine, HumanMine and TargetMine are integrated databases of genomic, expression and protein data for various organisms. Integrating data makes it possible to run sophisticated data mining queries that span domains of biological knowledge. This R package provides interfaces with these databases through webservices. It makes most from the correspondence of the data frame object in R and the table object in databases, while hiding the details of data exchange through XML or JSON.

Author: Bing Wang, Julie Sullivan, Rachel Lyne, Konstantinos Kyritsis, Celia Sanchez

Maintainer: InterMine Team <r.lyne at>

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


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:

InterMineR Vignette HTML R Script
Reference Manual PDF


biocViews AlternativeSplicing, ComparativeGenomics, DifferentialExpression, FunctionalGenomics, FunctionalPrediction, GO, GeneExpression, GeneRegulation, GeneSetEnrichment, GenomeAnnotation, GenomeWideAssociation, KEGG, Microarray, MultipleComparison, Pathways, Proteomics, Reactome, SNP, Software, SystemsBiology, Visualization
Version 1.26.0
In Bioconductor since BioC 3.6 (R-3.4) (6.5 years)
License LGPL
Depends R (>= 3.4.1)
Imports Biostrings, RCurl, XML, xml2, RJSONIO, sqldf, igraph, httr, S4Vectors, IRanges, GenomicRanges, SummarizedExperiment, methods
System Requirements
Bug Reports
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Suggests BiocStyle, Gviz, knitr, rmarkdown, GO.db,
Linking To
Depends On Me
Imports Me
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Package Archives

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

Source Package InterMineR_1.26.0.tar.gz
Windows Binary
macOS Binary (x86_64) InterMineR_1.26.0.tgz
macOS Binary (arm64) InterMineR_1.26.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Package Short Url
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Old Source Packages for BioC 3.19 Source Archive