CGHtest specifications

Information


Unique identifier OMICS_26999
Name CGHtest
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Version 1.1
Stability Stable
Maintained Yes

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CGHtest in publications

 (7)
PMCID: 5342020
PMID: 27729614
DOI: 10.18632/oncotarget.12510

[…] used for two-group comparisons of stage ii versus iii and relapse versus non-relapse tumors. chi-square tests on occurrence of cna between the two groups were performed including 10000 permutations (cghtest; www.few.vu.nl/~mavdwiel). separate tests were performed to compare frequencies of gains versus no-gains and losses versus no-losses. associations of cna regions to dfs were investigated […]

PMCID: 4873174
PMID: 27195705
DOI: 10.1371/journal.pone.0155840

[…] of 10 consecutive probes. the segmentation process was carried out using the dnacopy bioconductor package []. bioconductor´s cghcall package was employed for determining the step, and cghregions and cghtest packages[] were used to estimate genomic regions and false discovery rate, respectively., microarray and sequencing data have been deposited in geo and sra, under the following accession […]

PMCID: 5122336
PMID: 26993771
DOI: 10.18632/oncotarget.8058

[…] qdnaseq []. the sequencing data has been made available through the european nucleotide archive (ena; http://www.ebi.ac.uk/ena; dataset id: prjeb9176.), the χ2-test as available in the r-package cghtest was used to determine possible differences between chromosomal profiles of cell lines with a high immortalization capacity and cell lines with a low immortalization capacity []. the test […]

PMCID: 4281204
PMID: 25551557
DOI: 10.1371/journal.pone.0115835

[…] as described by van wieringen et al. with the “overlapplus” function. statistical differences between the matched series were determined using a wilcoxon test with ties using the r-package cghtest . apart from the expected higher frequency of 17p gain only one other chromosomal difference, a lower frequency of 7p gain, was observed (fdr q<0.05). no other significant differences […]

PMCID: 3668473
PMID: 23558894
DOI: 10.1038/bjc.2013.141

[…] nexus copy number v5.1 (biodiscovery, inc.). potentially group-specific alterations were defined using fisher's exact test (fet) (p-value<0.05) implemented in nexus and chi-square test within cghtest (r package) with correction for multiple testing (fdr<0.02)., the list of potentially group-specific regions was further refined using data from the tcga ovarian study () as described […]


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