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Number of citations per year for the bioinformatics software tool AgiMicroRna
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Protocols

AgiMicroRna specifications

Information


Unique identifier OMICS_07859
Name AgiMicroRna
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Agilent Technologies
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 2.30.0
Stability Stable
Requirements
limma, methods, gplots, Biobase, R(>=2.10), gtools, preprocessCore, marray, geneplotter, gdata, affy(>=1.22), affycoretools, codelink
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Pedro López-Romero

Publication for AgiMicroRna

AgiMicroRna citations

 (47)
library_books

Integrated miRNA mRNA spatial signature for oral squamous cell carcinoma: a prospective profiling study of Narrow Band Imaging guided resection

2018
Sci Rep
PMCID: 5770416
PMID: 29339786
DOI: 10.1038/s41598-018-19341-x

[…] of the bioinformatics pipeline is shown in Fig. . Expression data from 54 mRNA and 54 miRNA arrays were processed through discrete QC pipelines: mRNA via affyAnalysisQC and simpleaffy; miRNA via the AgiMicroRNA package. Good library quality and consistent hybridization quality were evident, however some data from both mRNA and miRNA arrays were identified as outliers and excluded from further pro […]

library_books

Transcriptomic analysis in pediatric spinal ependymoma reveals distinct molecular signatures

2017
Oncotarget
PMCID: 5777794
PMID: 29383182
DOI: 10.18632/oncotarget.23311

[…] iments with a small number of replicates []. Differential expression was defined for genes with FDR < 0.05.miRNA expression was profiled by Agilent microarrays, and processed and normalized using the AgiMicroRna R package (using between-array quantile normalization) []. To filter miRNAs with very low expression across most EPN samples, we removed miRNAs that were detected in < 25% of samples (usin […]

library_books

miRNA profiling of NurOwn®: mesenchymal stem cells secreting neurotrophic factors

2017
PMCID: 5678806
PMID: 29116031
DOI: 10.1186/s13287-017-0692-1

[…] tal RNA using Agilent’s miRNA platform (SurePrint G3 Human v16 microRNA 8 × 60K microarray slides, Agilent Technologies, Cheadle, UK). Data pre-processing and normalization was carried out using the “AgiMicroRNA” package in Bioconductor (https://www.bioconductor.org/packages/devel/bioc/vignettes/AgiMicroRna/inst/doc/AgiMicroRna.pdf). miRNAs differentially expressed between the MSC-NTF and MSC cell […]

library_books

Predicted effects of observed changes in the mRNA and microRNA transcriptome of lung neutrophils during S. pneumoniae pneumonia in mice

2017
Sci Rep
PMCID: 5595893
PMID: 28900269
DOI: 10.1038/s41598-017-11638-7

[…] ne ID, Refseq mRNA, and Genbank accession numbers. miR expression signals were extracted from microarray images using Agilent Feature Extraction (FE) software, and normalized using either LVSmiRNA or AgiMicroRna package from Bioconductor. These normalization methods were used based on literature suggesting distinct advantages offered by each in normalizing gene expression data–. LVSmiRNA uses the […]

library_books

MicroRNAs Clustered within the 14q32 Locus Are Associated with Endothelial Damage and Microparticle Secretion in Bicuspid Aortic Valve Disease

2017
Front Physiol
PMCID: 5591958
PMID: 28928672
DOI: 10.3389/fphys.2017.00648

[…] microarrays (deposited at Gene Expression Omnibus under GEO Series accession number GSE101616) were normalized using the robust multi-array average (RMA) method (Irizarry et al., ) implemented in the AgiMicroRna Bioconductor package, and the fold changes in circulating miRNAs were determined using the linear model implemented in the limma Bioconductor package (Ritchie et al., ). The Benjamini and […]

library_books

Low dose exposure to bisphenols A, F and S of human primary adipocyte impacts coding and non coding RNA profiles

2017
PLoS One
PMCID: 5476258
PMID: 28628672
DOI: 10.1371/journal.pone.0179583

[…] RNA data, a detection p-value was used to filter out non-expressed miRNA leading to consider 325 (differentiation) or 483 probes (BPs) as expressed. The normalization was performed with the R package AgiMicroRna []. […]


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AgiMicroRna institution(s)
Epidemiology, Atherothrombosis and Imaging Department Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Melchor Fernández Almagro, Madrid, Spain

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