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. 2019 Sep 1;35(17):3206-3207.
doi: 10.1093/bioinformatics/btz039.

InterMineR: an R package for InterMine databases

Konstantinos A Kyritsis  1   2   3 , Bing Wang  2   3 , Julie Sullivan  2   3 , Rachel Lyne  2   3 , Gos Micklem  2   3
Affiliations

InterMineR: an R package for InterMine databases

Konstantinos A Kyritsis et al. Bioinformatics. .

Abstract

Summary: InterMineR is a package designed to provide a flexible interface between the R programming environment and biological databases built using the InterMine platform. The package offers access to the flexible query builder and the library of term enrichment tools of the InterMine framework, as well as interoperability with other Bioconductor packages. This facilitates automation of data retrieval tasks as well as downstream analysis with existing statistical tools in the R environment.

Availability and implementation: InterMineR is free and open source, released under the LGPL licence and available from the Bioconductor project and Github (https://bioconductor.org/packages/release/bioc/html/InterMineR.html, https://github.com/intermine/interMineR).

Supplementary information: Supplementary data are available at Bioinformatics online.

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References

    1. Chang W. et al. (2017) shiny: Web Application Framework for R http://shiny.rstudio.com/.
    1. Feng G. et al. (2010) A collection of bioconductor methods to visualize gene-list annotations. BMC Res. Notes, 3, 10.. - PMC - PubMed
    1. Feng G. et al. (2012) Using the bioconductor GeneAnswers package to interpret gene lists. Methods Mol. Biol., 802, 101–112. - PubMed
    1. Gentleman R.C. et al. (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol., 5, R80.. - PMC - PubMed
    1. Huang L. et al. (2014) GeneAnswers: Integrated Interpretation of Genes https://www.bioconductor.org/packages/release/bioc/html/GeneAnswers.html Version 2.24

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