iMir statistics

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Citations per year

Number of citations per year for the bioinformatics software tool iMir

Tool usage distribution map

This map represents all the scientific publications referring to iMir per scientific context
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Associated diseases


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iMir specifications


Unique identifier OMICS_00358
Name iMir
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java, Perl, Python, R
License GNU General Public License version 2.0
Computer skills Advanced
Stability No
Maintained No


No version available

Publication for iMir

iMir citations


Genome wide profiling of the PIWI interacting RNA mRNA regulatory networks in epithelial ovarian cancers

PLoS One
PMCID: 5761873
PMID: 29320577
DOI: 10.1371/journal.pone.0190485

[…] piRNAs which are excluded from the analysis (). In contrast, DE piRNAs of SOCa includes 56 up-regulated and 81 down-regulated piRNAs excluding 6 piRNAs showing anomalous expression as predicted from iMir and mirTools2 (). Surprisingly, 55% of DE piRNAs in ENOCa and 27% of DE piRNAs in SOCa were found to originate from intronic regions which hint towards the fact that introns probably contribute t […]


miRNome Profiling in Bicuspid Aortic Valve Associated Aortopathy by Next Generation Sequencing

Int J Mol Sci
PMCID: 5713463
PMID: 29165337
DOI: 10.3390/ijms18112498

[…] ed by normalization with the total reads of all called miRNAs in the sample. Sequencing data was trimmed to remove adapter sequences and aligned against a human reference database (miRBase v20) using iMir software, a reliable, flexible and fully automated workflow, useful for rapidly and efficiently analyzing high-throughput small RNA-Seq data [].Identification and analysis of differentially expre […]


Integrating Epigenomics into the Understanding of Biomedical Insight

Bioinform Biol Insights
PMCID: 5138066
PMID: 27980397
DOI: 10.4137/BBI.S38427

[…] the known ncRNAs quantification and novel ncRNAs identification by inferring annotation databases, following the functional interaction analysis based on structural features and database annotations. iMir is such an integrated pipeline with graphical user interface (GUI) that allows ncRNAs’ identification such as miRNA and piRNA by miRAnalyzer or miRDeep2, differential expression analysis by DESeq […]


Specific patterns of PIWI interacting small noncoding RNA expression in dysplastic liver nodules and hepatocellular carcinoma

PMCID: 5342370
PMID: 27429044
DOI: 10.18632/oncotarget.10567
call_split See protocol

[…] llumina TruSeq smallRNA sample preparation Kit and each library (8pM) was sequenced on HiSeq2500 (Illumina) for 50 cycles at Genomix4life ( SmallRNA-Seq data were analyzed using iMir [], see Supplementary Materials and Methods for bioinformatics analyses. Raw smallRNA-Seq data are available in ArrayExpress database ( with accession: E-MTAB- […]


A survey of best practices for RNA seq data analysis

Genome Biol
PMCID: 4728800
PMID: 26813401
DOI: 10.1186/s13059-016-0881-8

[…] uch as miRDeep [] and miRDeep-P [] for animal and plant miRNAs, respectively, or the trans-acting siRNA prediction tool at the UEA sRNA Workbench []. Tools such as miRTools 2.0 [], ShortStack [], and iMir [] also exist for comprehensive annotation of sRNA libraries and for identification of diverse classes of sRNAs. […]


MiRNAs and piRNAs from bone marrow mesenchymal stem cell extracellular vesicles induce cell survival and inhibit cell differentiation of cord blood hematopoietic stem cells: a new insight in transplantation

PMCID: 4872742
PMID: 26760763
DOI: 10.18632/oncotarget.6791

[…] d for library preparation with Illumina TruSeq small RNA sample preparation Kit. The library (10 pM) was sequenced on HiSeq1000 (Illumina) for 50 cycles. Small RNA sequencing data were analyzed using iMir [] and mature miRNA list obtained with miRanalyzer [] was used to characterize EVs small RNA content. Mature microRNAs with a readCount less than 5 were removed. Final mature microRNAs readCount […]

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iMir institution(s)
Laboratory of Molecular Medicine and Genomics, Department of Medicine and Surgery, University of Salerno, Salerno, Baronissi, Italy

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