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RmiR specifications


Unique identifier OMICS_00789
Name RmiR
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 1.36.0
Stability Stable
methods, stats, org.Hs.eg.db, DBI, R(>=2.7.0), RmiR.Hs.miRNA, RSVGTipsDevice, hgug4112a.db
Maintained Yes




No version available



  • person_outline Francesco Favero

RmiR citations


Application of microRNA and mRNA expression profiling on prognostic biomarker discovery for hepatocellular carcinoma

BMC Genomics
PMCID: 4046763
PMID: 24564407
DOI: 10.1186/1471-2164-15-S1-S13

[…] By the RmiR [] package in Bioconductor, we obtained the targeting relationships between microRNAs and genes that appear in at least three microRNA target databases from six: miRBase [], TargetScan [], miRand […]


Integrated genomic analysis of triple negative breast cancers reveals novel microRNAs associated with clinical and molecular phenotypes and sheds light on the pathways they control

BMC Genomics
PMCID: 4008358
PMID: 24059244
DOI: 10.1186/1471-2164-14-643

[…] For each miRNA, candidate targets were inferred using data from six different databases (miRanda, PicTar, TargetScan, mirBase, miRTarget2, TarBase[-]) using the RmiR package from R Bioconductor (http://www.bioconductor.org/).For confirmatory evaluation of our results regarding the influence of individual miRNAs on gene sets/pathways, we used the miRTarBase, a […]


MicroRNA expression signature in human abdominal aortic aneurysms

BMC Med Genomics
PMCID: 3507654
PMID: 22704053
DOI: 10.1186/1755-8794-5-25

[…] ds of miRNA are usually degraded upon uploading of the miRNA duplex into the RISC complex []. The miRNA target prediction databases TargetScan, MirTarget2, and Pictar were queried using the R package RmiR.hsa []. The predicted targets were then compared to a list of upregulated genes found in our previous study []. In addition, we queried targets of miR-331-3p from TargetScan's non-conserved targe […]


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