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MetaQC specifications

Information


Unique identifier OMICS_04032
Name MetaQC
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 0.1.13
Stability Stable
Requirements
gtools, survival, foreach, matrixStats, gdata, R(≥2.10.0), proto, iterators, doMC, doSNOW, FactoMineR
Maintained Yes

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Documentation


Publication for MetaQC

MetaQC in publications

 (15)
PMCID: 5802200
PMID: 29328377
DOI: 10.3892/mmr.2018.8398

[…] metastatic breast cancer samples. a total of 5 expression profiles of metastatic breast cancer samples were downloaded from the gene expression omnibus database, which were then analyzed using the metaqc and metade packages in r language. the feature genes between metastasis and non-metastasis samples were screened under the threshold of p<0.05. based on the protein-protein interactions […]

PMCID: 5819940
PMID: 29328363
DOI: 10.3892/ijmm.2018.3359

[…] (limma; http://www.biocon-ductor.org/packages/release/bioc/html/limma.html) package version 3.22.1 was then used to normalize the data ()., to eliminate the bias from different platforms, the metaqc package version 0.1.13 was utilized to perform quality control of the different datasets, in combination with principal component analysis and standardized mean rank (). the standards […]

PMCID: 5819923
PMID: 29286069
DOI: 10.3892/ijmm.2017.3332

[…] to identify differentially expressed genes (degs) between stage i and ii lung squamous carcinoma samples in seven microarray datasets collected from the gene expression omnibus database via the metaqc and metade package in r. the important degs were selected according to the betweenness centrality value of the protein-protein interaction (ppi) network. support vector machine (svm) analysis […]

PMCID: 5780129
PMID: 29115420
DOI: 10.3892/mmr.2017.7850

[…] using the quality control standards [including external quality control, internal quality control, consistency quality control (cqcg and cqcp) and accuracy quality control (aqcg and aqcp)] in the metaqc package (), quality control was performed for the datasets. to identify reliable datasets, the datasets were further assessed and screened using the two-dimensional diagram of principal […]

PMCID: 5627885
PMID: 28901446
DOI: 10.3892/ijmm.2017.3126

[…] (os) were analyzed to identify critical genes associated with metastasis. five gene expression datasets were screened and downloaded from gene expression omnibus (geo). following assessment by metaqc, the dataset gse9508 was excluded for poor quality. subsequently, differentially expressed genes (degs) between metastatic and non-metastatic os were identified using meta-analysis. […]


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MetaQC institution(s)
Department of Biostatistics, University of Pittsburgh, Pittsburgh, USA

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