An R package for accessing miRBase mature database, based on R package/framework biodb.
This package is an extension of biodb that implements a connector to miRBase mature database.
Install the latest version of this package by running the following commands:
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install('biodbMirbase')To instantiate a connector to miRBase mature database, run:
mybiodb <- boidb::newInst()
conn <- mybiodb$getFactory()$createConn('mirbase.mature')
mybiodb$terminate()To get documentation on the implemented connector, run the following command in R:
?biodbMirbase::MirbaseMatureConn- Ana Kozomara, Sam Griffiths-Jones. (2013) miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Research, Volume 42, Issue D1, 1 January 2014, Pages D68–D73, https://doi.org/10.1093/nar/gkt1181.
- Ana Kozomara, Sam Griffiths-Jones. (2010) miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Research, Volume 39, Issue suppl_1, 1 January 2011, Pages D152–D157, https://doi.org/10.1093/nar/gkq1027.
- Sam Griffiths-Jones, Harpreet Kaur Saini, Stijn van Dongen, Anton J. Enright. (2007) miRBase: tools for microRNA genomics. Nucleic Acids Research, Volume 36, Issue suppl_1, 1 January 2008, Pages D154–D158, https://doi.org/10.1093/nar/gkm952.
- Sam Griffiths-Jones, Russell J. Grocock, Stijn van Dongen, Alex Bateman, Anton J. Enright. (2006) miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Research, Volume 34, Issue suppl_1, 1 January 2006, Pages D140–D144, https://doi.org/10.1093/nar/gkj112.