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iMir specifications

Information


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

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Publication for iMir

iMir in pipeline

2018
PMCID: 5761873
PMID: 29320577
DOI: 10.1371/journal.pone.0190485

[…] sequences (hg19) used for this purpose were downloaded from the ucsc genome browser., the uniquely mapped reads showing length distribution within the range of 16–40 nts were analyzed using imir [] and mirtools2.0 [] to predict known and novel pirnas as well as mirnas and their differential expression with respect to normal ovarian tissue as a control. the annotations of genomic regions […]


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iMir in publications

 (5)
PMCID: 5761873
PMID: 29320577
DOI: 10.1371/journal.pone.0190485

[…] sequences (hg19) used for this purpose were downloaded from the ucsc genome browser., the uniquely mapped reads showing length distribution within the range of 16–40 nts were analyzed using imir [] and mirtools2.0 [] to predict known and novel pirnas as well as mirnas and their differential expression with respect to normal ovarian tissue as a control. the annotations of genomic regions […]

PMCID: 5713463
PMID: 29165337
DOI: 10.3390/ijms18112498

[…] 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 […]

PMCID: 5138066
PMID: 27980397
DOI: 10.4137/BBI.S38427

[…] 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 […]

PMCID: 5342370
PMID: 27429044
DOI: 10.18632/oncotarget.10567

[…] truseq smallrna sample preparation kit and each library (8pm) was sequenced on hiseq2500 (illumina) for 50 cycles at genomix4life (www.genomix4life.com). smallrna-seq data were analyzed using imir [], see supplementary materials and methods for bioinformatics analyses. raw smallrna-seq data are available in arrayexpress database (https://www.ebi.ac.uk/arrayexpress/) with accession: […]

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

[…] 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., the last step in a standard transcriptomics study (fig. ) is often […]


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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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