DOI: 10.18129/B9.bioc.InterMineR    

R Interface with InterMine-Powered Databases

Bioconductor version: Release (3.9)

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

Maintainer: InterMine Team <j.sullivan at>

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


To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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:



HTML R Script Enrichment Analysis and Visualization
HTML R Script FlyMine Genomic Visualizations
HTML R Script InterMineR Vignette
PDF   Reference Manual
Text   NEWS


biocViews AlternativeSplicing, ComparativeGenomics, DifferentialExpression, FunctionalGenomics, FunctionalPrediction, GO, GeneExpression, GeneRegulation, GeneSetEnrichment, GenomeAnnotation, GenomeWideAssociation, KEGG, Microarray, MultipleComparison, Pathways, Proteomics, Reactome, SNP, Software, SystemsBiology, Visualization
Version 1.6.1
In Bioconductor since BioC 3.6 (R-3.4) (2 years)
License LGPL
Depends R (>= 3.4.1)
Imports Biostrings, RCurl, XML, xml2, RJSONIO, sqldf, igraph, httr, S4Vectors, IRanges, GenomicRanges, SummarizedExperiment, methods
Suggests BiocStyle, Gviz, knitr, rmarkdown, GeneAnswers, GO.db,
Depends On Me
Imports Me
Suggests Me
Links To Me
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Source Package InterMineR_1.6.1.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) InterMineR_1.6.1.tgz
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