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HTqPCR specifications

Information


Unique identifier OMICS_02314
Name HTqPCR
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Version 1.34.0
Stability Stable
Requirements
limma, methods, stats, RColorBrewer, gplots, graphics, Biobase, utils, stats4, grDevices, affy, statmod
Maintained Yes

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Documentation


Publication for HTqPCR

HTqPCR in publications

 (63)
PMCID: 5922374
PMID: 29721180
DOI: 10.18632/oncotarget.24874

[…] were visualized using clarity ecl western blot substrate (biorad) according to the manufacturer’s instructions., analysis of mirna cq values from high-throughput qpcr assays was conducted using the htqpcr package [] of bioconductor [], which runs on r statistical computing environment (http://www.r-project.org/). difference in mirna expression levels in bm resident cells from the three groups […]

PMCID: 5864010
PMID: 29566027
DOI: 10.1371/journal.pone.0194530

[…] i+ii, v2.r)., totally, due to the complexity of disease and to increase the power of the analyses, three different strategies based on the r (3.2.3) bioconductor (3.2) packages of limma (3.26.9) [], htqpcr (1.24.0) [] and r cran package of mcmc (0.9–5) [] were tested to get insight into the performance of the methods. among these, htqpcr package was the most reliable package, […]

PMCID: 5858605
PMID: 29593587
DOI: 10.3389/fpsyt.2018.00081

[…] one of the most stably expressed mirnas circulating in human plasma (). a log2 fold-change ratio (δδct value) of expression was calculated using mean values of control samples as a calibrator in the htqpcr package in bioconductor (). the relative quantification (rq) of each mirna target was defined as 2−δδct. for hypothetical testing of the difference in expression between two groups, we applied […]

PMCID: 5842524
PMID: 29514634
DOI: 10.1186/s12864-018-4520-5

[…] measure the expression of selected genes using real-time pcr analysis user guide pn 68000088 k1. primers used for qpcr reactions are listed in additional file . data were analyzed using htqpcr r package [] and normalized considering gapdh, rps8 and top2b as reference genes, as suggested after genorm analysis []., the activity of fatty acid synthase (fasn), a key lipogenic enzyme, […]

PMCID: 5820326
PMID: 29463868
DOI: 10.1038/s41598-018-21337-6

[…] step was performed to evaluate the replicate’s performance. principal component analysis (pca), heat-maps, cluster dendrograms and boxplots of raw and normalized ct values were assessed using the htqpcr platform (bioconductor)., to measure differential expression, limma package was used for statistical analysis and false discovery rate (fdr) correction. fold change was computed based […]


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HTqPCR institution(s)
EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK

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