HTqPCR statistics

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Citations per year

Number of citations per year for the bioinformatics software tool HTqPCR
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Tool usage distribution map

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

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Protocols

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

Versioning


No version available

Documentation


Publication for HTqPCR

HTqPCR citations

 (63)
library_books

miRNA expression profile of bone marrow resident cells from children with neuroblastoma is not significantly different from that of healthy children

2018
Oncotarget
PMCID: 5922374
PMID: 29721180
DOI: 10.18632/oncotarget.24874

[…] 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 of […]

library_books

MicroRNA expression in serum samples of sulfur mustard veterans as a diagnostic gateway to improve care

2018
PLoS One
PMCID: 5864010
PMID: 29566027
DOI: 10.1371/journal.pone.0194530

[…] 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, and had the advantag […]

library_books

Circulating MicroRNA Expression Levels Associated With Internet Gaming Disorder

2018
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 […]

library_books

Multi tissue transcriptomic study reveals the main role of liver in the chicken adaptive response to a switch in dietary energy source through the transcriptional regulation of lipogenesis

2018
BMC Genomics
PMCID: 5842524
PMID: 29514634
DOI: 10.1186/s12864-018-4520-5

[…] imultaneously 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 []. […]

library_books

CD38 promotes pristane induced chronic inflammation and increases susceptibility to experimental lupus by an apoptosis driven and TRPM2 dependent mechanism

2018
Sci Rep
PMCID: 5820326
PMID: 29463868
DOI: 10.1038/s41598-018-21337-6

[…] ity 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). […]

call_split

Heterogeneous muscle gene expression patterns in patients with massive rotator cuff tears

2018
PLoS One
PMCID: 5749784
PMID: 29293645
DOI: 10.1371/journal.pone.0190439
call_split See protocol

[…] nalyses were performed based on the groups identified by hierarchical clustering and confirmed by PCA.Differential expression values (delta-delta-Ct)[] were calculated with the limmaCtData wrapper in HTqPCR for the Bioconductor package limma using a moderated t-test[]. Based on the cluster analysis and histological data available for the RSA biopsies, the intact comparisons described below include […]


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

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