The multiMiR R package and database:
Integration of microRNA-target interactions along with their disease and drug associations
(Nucleic Acids Res. 2014 Jul 24. pii: gku631)
SummarymicroRNAs (miRNAs) regulate expression by promoting degradation or repressing translation of target transcripts. miRNA target sites have been catalogued in databases based on experimental validation and computational prediction using a variety of algorithms. Several online resources provide collections of multiple databases but need to be imported into other software, such as R, for processing, tabulation, graphing and computation. Currently available miRNA target site packages in R are limited in the number of databases, types of databases and flexibility.
The R package multiMiR, with web server at http://multimir.ucdenver.edu, is a comprehensive collection of predicted and validated miRNA-target interactions and their associations with diseases and drugs.
|Category||External Database||Version||Last Update||Human Records||Mouse Records||Rat Records||Total Records|
|Validated miRNA-target Interactions||miRecords||4||Apr 27, 2013||2425||449||171||3045|
|Predicted miRNA-target Interactions||DIANA-microT-CDS||5||Sept, 2013||7664602||3747171||0||11411773|
|PicTar||2||Dec 21, 2012||404066||302236||0||706302|
|PITA||6||Aug 31, 2008||7710936||5163153||0||12874089|
|miRNA-disease/drug Associations||miR2Disease||N/A||Mar 14, 2011||2875||0||0||2875|
|Pharmaco-miR (Verified Sets)||N/A||N/A||308||5||0||313|
|PhenomiR||2||Feb 15, 2011||15138||491||0||15629|
The current version of the multiMiR R Package is 0.99.5 and can be downloaded from
Note: The version of the R package and Database have been seperated. The R package has
been set back to 0.99 while the Database will continue from v2.1. The R package will now
allow you to choose pevious database versions if desired to reproduce previous results.
multiMiR requires the XML and RCurl packages from R. The packages can be installed from R by typing:
# To install multiMiR, first install suggested package BiocStyle
# Now install devtools (for installing from GitHub repositories)
# Now install the development version of the multiMiR package
devtools::install_github("kechrislab/multimir", build_vignettes = TRUE)
multiMiR is distributed with a Userís Guide illustrating examples of package functions and queries.
The User's Guide can be downloaded here or viewed from R by typing: