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Protocols

ReadqPCR specifications

Information


Unique identifier OMICS_03936
Name ReadqPCR
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Version 1.26.0
Stability Stable
Requirements
methods, Biobase, R(>=2.14.0), affy, qpcR
Maintained Yes

Versioning


No version available

Documentation


Publication for ReadqPCR

ReadqPCR citations

 (11)
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Small ocean temperature increases elicit stage dependent changes in DNA methylation and gene expression in a fish, the European sea bass

2017
Sci Rep
PMCID: 5622125
PMID: 28963513
DOI: 10.1038/s41598-017-10861-6
call_split See protocol

[…] re calculated using the RQ Manager 1.2.1 (Applied Biosystems). Measured Cq values were corrected for primer efficiency CqE = Cq(log(1+E)/log2) and further analyses were performed using the R packages ReadqPCR (version 1.16.0) and NormqPCR (version 1.16.0). The geometric mean of the two reference genes was used to normalize the expression of target genes. Relative gene expression was calculated usi […]

call_split

Reversing Age Related Changes of the Laryngeal Muscles by Chronic Electrostimulation of the Recurrent Laryngeal Nerve

2016
PLoS One
PMCID: 5125708
PMID: 27893858
DOI: 10.1371/journal.pone.0167367
call_split See protocol

[…] by melting curve analysis. Quantitation cycle (Cp) values were obtained using the AbsQuant/2nd Derivative Max method of the LightCycler® 480 software and were further processed using the R packages “ReadqPCR” and “NormqPCR”. Cp values from technical triplicates were averaged. Several candidate internal reference RNAs were analysed in preliminary experiments using the geNorm algorithm [], resultin […]

library_books

Increased intracellular pH is necessary for adult epithelial and embryonic stem cell differentiation

2016
PMCID: 5100294
PMID: 27821494
DOI: 10.1083/jcb.201606042

[…] 11760; Invitrogen) according to the manufacturer’s protocol on a Real-Time PCR Viaa7 instrument (Applied Biosystems). Quantitative PCR analysis was done in the open source RStudio software using the ReadqPCR and NormqPCR (). Open source packages are available on the Bioconductor website. For each gene, three to five independent cell preparations were used. […]

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Genome wide association study in essential tremor identifies three new loci

2016
PMCID: 5382938
PMID: 27797806
DOI: 10.1093/brain/aww242
call_split See protocol

[…] Mix (Thermo Fisher). We performed at least two technical replicates in one qPCR run (four replicates in two qPCR runs for ACTB, PCP2 and STK32B). We calculated expression using bioconductor packages ReadqPCR and NormqPCR. Technical replicates were averaged, then gene-expression was normalized using ACTB and PCP2 and expression differences assessed using Student’s t-test. […]

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The Expression of Inflammatory Mediators in Bladder Pain Syndrome

2016
PMCID: 4926725
PMID: 26965559
DOI: 10.1016/j.eururo.2016.02.058
call_split See protocol

[…] sion levels of 96 inflammatory mediators in disease versus control tissue calculated using the ΔCT (cycle time) method and normalised against the geometric mean of three housekeeping genes using the ReadqPCR and NormqPCR packages . […]

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Identification and Validation of Reference Genes for RT qPCR Studies of Hypoxia in Squamous Cervical Cancer Patients

2016
PLoS One
PMCID: 4887009
PMID: 27244197
DOI: 10.1371/journal.pone.0156259
call_split See protocol

[…] ce level was 5% unless otherwise indicated, and all P-values were two-sided.All analyses were performed using R [] version 3.1.1. For geNorm analyses, the read.qPCR() and selectHKs() functions in the ReadqPCR and NormqPCR packages [] were applied. For the NormFinder analyses the Normfinder() function provided by Molecular Diagnostic Laboratory, Department of Molecular Medicine, Aarhus University H […]

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ReadqPCR institution(s)
Institute of Structural and Molecular Biology, University College of London, London, UK

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