cghMCR statistics

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cghMCR specifications

Information


Unique identifier OMICS_00710
Name cghMCR
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 1.18.0
Stability Stable
Requirements
limma, methods, DNAcopy, stats4, CNTools, BiocGenerics(>=0.1.6)
Maintained Yes

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Documentation


cghMCR in publications

 (14)
PMCID: 5829240
PMID: 29487377
DOI: 10.1038/s41598-018-22126-x

[…] the determination of the cutoffs. used cutoffs for the samples are given in the supplementary table . the frequently altered regions in the cohort were determined using the r packages cntools and cghmcr. losses seen in more than 20%, and gains in more than 25% of the samples were included for further analyses (supplementary fig.  and supplementary table ). after determining the frequently […]

PMCID: 5628952
PMID: 28939077
DOI: 10.1016/j.oraloncology.2017.08.003

[…] high fraction (53%) ( fig. 2b), which is much higher than observed in various cancers (15–26%) not associated with tobacco and consistent with reports in hnscc , .fig. 1, we used control-freec and cghmcr package to identify genomic regions harboring statistically significant copy number gains and losses relative to normal tissues. 440 amplified and 2275 deleted regions were identified across […]

PMCID: 5515741
PMID: 28700469
DOI: 10.1097/MD.0000000000007264

[…] (bh) method.[] only genes meeting the selection criteria of |logfc (fold change)| ≥0.5 and adjusted p value <.05 were considered degs., raw acgh data were preprocessed using the package cghmcr in r (version 1.34.0, http://www.bioconductor.org/packages/release/bioc/html/cghmcr.html).[,] the method “minimum” in the package was used for background correction, and this method meant […]

PMCID: 5588164
PMID: 28928828
DOI: 10.3892/ol.2017.6519

[…] and differentially methylated regions were screened with methyanalysis in r. copy number analysis was performed and genes with copy number gains/losses were further screened using dnacopy and cghmcr packages. functional enrichment analyses were performed using the database for annotation, visualization and integrated discovery online tool, and protein-protein interactions were identified […]

PMCID: 5452530
PMID: 28569140
DOI: 10.1186/s12859-017-1705-x

[…] calling cnv segments across the genome., for the gene-based comparison, we first annotated the detected cnv segments in the benchmark and samples for both real data and simulated data. we used “cghmcr” r package from bioconductor [] to identify cnv genes using refseq gene identifications. the average of the cnv values of the overlapping cnv segments for each gene is used as the gene cnv […]


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