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qcmetrics specifications

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Unique identifier OMICS_02032
Name qcmetrics
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.18.0
Stability Stable
Requirements
AnnotationDbi, methods, Biobase, S4Vectors, BiocStyle, lattice, tools, ggplot2, affy, R(>=3.3), knitr, xtable, Nozzle.R1, pander, MSnbase, yaqcaffy, MAQCsubsetAFX, RforProteomics, mzR, hgu133plus2cdf
Maintained Yes

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qcmetrics in publications

 (3)
PMCID: 5486189
PMID: 28680748
DOI: 10.1080/2162402X.2017.1316439

[…] of the normal value of at least three consecutive probes, and the mapping positions refer to the genome assembly hg19 (build 37). the quality of the test was assessed on the strength of the qcmetrics values. polymorphisms (http://projects.trag.ca/variation/) were not included because considered normal variants., total rna was extracted using trizol reagent (thermo fisher scientific). […]

PMCID: 4914342
PMID: 26909610
DOI: 10.18632/oncotarget.7541

[…] scanner (g2565ba). log2 ratios were determined with agilent feature extraction software (v9.1.3.1). the global quality of the individual microarrays was validated against the quality metrics (qcmetrics) provided in this software. results were analyzed with agilent's cgh analytics v3.5 software. copy number aberrations (cna) were detected using the aberration detection method algorithm 2 […]

PMCID: 4510819
PMID: 25690415
DOI: 10.1002/pmic.201400392

[…] generate reports (using sweave [] or knitr [,]) that contain the description of the analysis, the calculations and the visualizations. an example of such report generation is described in the qcmetrics package [] for raw ms data and 15n metabolic labeling quality control., it is important to emphasize that effective visualization is not about mastering a specific tool, programming […]

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