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CGH-Explorer specifications

Information


Unique identifier OMICS_02054
Name CGH-Explorer
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Stability Stable
Maintained Yes

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CGH-Explorer citations

 (20)
library_books

Assessment of established techniques to determine developmental and malignant potential of human pluripotent stem cells

2018
PMCID: 5954055
PMID: 29765017
DOI: 10.1038/s41467-018-04011-3

[…] to examine expression bias. the 10% most variable genes, calculated by the sum of squares of relative expression value for each gene, were removed during the analysis. data were processed using cgh-explorer (http://www.softgenetics.com/cghexplorer.html). a moving-average plot was generated using the moving average fit tool, with windows of 300 genes., esnp-karyotyping was performed […]

library_books

ID3 regulates the MDC1 mediated DNA damage response in order to maintain genome stability

2017
PMCID: 5638908
PMID: 29026069
DOI: 10.1038/s41467-017-01051-z

[…] probe signal intensities were calculated and plotted vs. genomic position using roche nimblegen’s nimblescan v2.5 software. data are displayed and analyzed in roche nimblegen signalmap software and cgh-explorer v2.55., hela cells were transiently transfected with control or id3 sirna. after 48 h of transfection, cells were exposed to ir for 3 h and then placed in 100 ng ml−1 […]

library_books

Patient derived xenografts undergo murine specific tumor evolution

2017
PMCID: 5659952
PMID: 28991255
DOI: 10.1038/ng.3967

[…] generated using the copy number workflow of the partek genomics suite software (http://www.partek.com/pgs), as reported by the original studies. cna profiles from cgh arrays were generated using the cgh-explorer software (http://heim.ifi.uio.no/bioinf/projects/cghexplorer/), using the program’s piecewise constant fit (pcf) algorithm, with the following set of parameters: least allowed deviation […]

library_books

Analysis of chromosomal aberrations and recombination by allelic bias in RNA Seq

2016
PMCID: 4941052
PMID: 27385103
DOI: 10.1038/ncomms12144

[…] values was calculated for each transcript and the 10% most variable genes were removed from further analysis. the data were processed and visualized using a cgh analysis software programme, cgh-explorer (http://heim.ifi.uio.no/bioinf/projects/cghexplorer/). gene expression regional bias was detected using the piecewise constant fit algorithm, using a set of parameters as follows: least […]

library_books

The landscape of chromosomal aberrations in breast cancer mouse models reveals driver specific routes to tumorigenesis

2016
PMCID: 4932194
PMID: 27374210
DOI: 10.1038/ncomms12160

[…] tissue samples were not available), was subtracted from the expression value of that gene in each sample to obtain a comparative value. the data were processed using a cgh analysis software program, cgh-explorer (http://heim.ifi.uio.no/bioinf/projects/cghexplorer/). gene expression regional biases were detected using the program's piecewise constant fit (pcf) algorithm, with the following set […]

library_books

miR146a mediated targeting of FANCM during inflammation compromises genome integrity

2016
PMCID: 5216775
PMID: 27351285
DOI: 10.18632/oncotarget.10275

[…] probe signal intensities were calculated and plotted versus genomic position using roche nimblegen nimblescan v2.5 software. data are displayed and analyzed in roche nimblegen signalmap software and cgh-explorer v2.55., ges-1 cells were labeled with 25 μm 5-iodo-2′-deoxyuridine (idu) for 20 min, followed by exposure to 5 mm hu for 5 h, and chased with 250 μm 5-chloro-2′-deoxyuridine (cldu) […]


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