snapCGH statistics

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Associated diseases

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snapCGH specifications

Information


Unique identifier OMICS_00734
Name snapCGH
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 1.50.0
Stability Stable
Requirements
limma, methods, stats, graphics, DNAcopy, utils, grDevices, cluster, aCGH, GLAD, tilingArray
Maintained Yes

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Documentation


snapCGH in publications

 (17)
PMCID: 5788600
PMID: 29416732
DOI: 10.18632/oncotarget.22804

[…] g3 human cgh microarray kit and arraycgh results were deposited in geo under accession number gse88947. after normalization we included a segmentation step using “rundnacopy” from the packages snapcgh and dnacopy (version 1.44.0) with alpha set to 0.01 and smooth region to 10. merging was performed using “mergestates” from (package snapcgh) with merge type set to 2 and default parameters. […]

PMCID: 5327725
PMID: 28202506
DOI: 10.15252/msb.20167159

[…] at the ucla pathology clinical microarray core. bioconductor analysis tools were used for data processing: moving minimum background correction and print‐tip loess normalization were performed in snapcgh package (smith et al, ); circular binary segmentation (with a minimum of three markers per segment) was performed on smoothed and log2‐transformed copy number profiles using dnacopy package […]

PMCID: 5485221
PMID: 28166199
DOI: 10.1038/onc.2016.507

[…] tumor specimens under irb-approved guidelines and grown as previously described. all cells were mycoplasma-free., gene-level copy number variation was estimated using the cbs algorithm from the 'snapcgh' package for r. gene dosage segments were classified as chromosomal ‘gain’ or ‘loss’ if the absolute value of the predicted dosage was more than 0.75 times the interquartile range […]

PMCID: 5063805
PMID: 27773988
DOI: 10.4137/CIN.S39368

[…] position, replicate probes were summarized by their median value, and missing values (generated by negative intensities in the normalization) were imputed using the loess procedure included in the snapcgh bioconductor r package., two pooled references were generated, one using the median intensities across the hapmap individuals and another for the normals and tumors, using the median […]

PMCID: 4278258
PMID: 25552933
DOI: 10.7150/ijbs.10583

[…] in the r programming language (version 2.15.0; www.r-project.org). signal intensities were preprocessed by the agilent feature extraction software followed by segmentation analysis using the snapcgh (version 1.26.0) r package available at the bioconductor (www.bioconductor.org) as previously reported . in brief, sex chromosomes were excluded from the arraycgh analysis […]


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