miRNAmeConverter: an R/bioconductor package for translating mature miRNA names to different miRBase versions.

Haunsberger, Stefan J.; Connolly, Niamh M.; Prehn, Jochen HM

miRNAmeConverter: an Rbioconductor package for translating matur.pdf (290.46 kB)

miRNAmeConverter: an R/bioconductor package for translating mature miRNA names to different miRBase versions.

Version 2 2021-04-12, 16:06

Version 1 2019-11-22, 16:50

journal contribution

posted on 2019-11-22, 16:50 authored by Stefan J. Haunsberger, Niamh M. Connolly, Jochen HM Prehn

Summary: The miRBase database is the central and official repository for miRNAs and the current release is miRBase version 21.0. Name changes in different miRBase releases cause inconsistencies in miRNA names from version to version. When working with only a small number of miRNAs the translation can be done manually. However, with large sets of miRNAs, the necessary correction of such inconsistencies becomes burdensome and error-prone. We developed miRNAmeConverter , available as a Bioconductor R package and web interface that addresses the challenges associated with mature miRNA name inconsistencies. The main algorithm implemented enables high-throughput automatic translation of species-independent mature miRNA names to user selected miRBase versions. The web interface enables users less familiar with R to translate miRNA names given in form of a list or embedded in text and download of the results.

Availability and Implementation: The miRNAmeConverter R package is open source under the Artistic-2.0 license. It is freely available from Bioconductor ( http://bioconductor.org/packages/miRNAmeConverter ). The web interface is based on R Shiny and can be accessed under the URL http://www.systemsmedicineireland.ie/tools/mirna-name-converter/ . The database that miRNAmeConverter depends on is provided by the annotation package miRBaseVersions.db and can be downloaded from Bioconductor ( http://bioconductor.org/packages/miRBaseVersions.db ). Minimum R version 3.3.0 is required.

Contact: stefanhaunsberger@rcsi.ie.

Supplementary information: Supplementary data are available at Bioinformatics online.

Funding

This work was supported by the Science Foundation Ireland research grants 12/COEN/18—Joint Programming in Neurodegenerative Disorders, COEN-Phase II, ‘Neuro-miR’ and 13/IA/1881 to J.H.M.P.

History

Comments

This is a pre-copyedited, author-produced PDF of an article accepted for publication in Bioinformatics following peer review. The version of record Haunsberger SJ, Connolly NM, Prehn JH. miRNAmeConverter: an R/bioconductor package for translating mature miRNA names to different miRBase versions. Bioinformatic.2017;33(4):592-593 is available online at: https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btw660

Published Citation

Haunsberger SJ, Connolly NM, Prehn JH. miRNAmeConverter: an R/bioconductor package for translating mature miRNA names to different miRBase versions. Bioinformatic.2017;33(4):592-593.