Type

Journal Article

Authors

Jochen H M Prehn
Niamh M C Connolly
Stefan J Haunsberger

Subjects

Computer Science

Topics
mirna names open source mature high throughput algorithm web translating

miRNAmeConverter: an R/Bioconductor package for translating mature miRNA names to different miRBase versions. (2016)

Abstract 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. 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://neuromir.eu/tools-for-research/mirnameconverter/ 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. stefanhaunsberger@rcsi.ie.
Collections Ireland -> Royal College of Surgeons in Ireland -> PubMed

Full list of authors on original publication

Jochen H M Prehn, Niamh M C Connolly, Stefan J Haunsberger

Experts in our system

1
Jochen H M Prehn
Royal College of Surgeons in Ireland
Total Publications: 206
 
2
Niamh M C Connolly
Royal College of Surgeons in Ireland
Total Publications: 14