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CGHcall specifications


Unique identifier OMICS_00709
Name CGHcall
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 2.20.0
Stability Stable
methods, Biobase, R(>=2.0.0), impute(>=1.8.0), DNAcopy(>=1.6.0), CGHbase(>=1.15.1), snowfall
Maintained Yes


No version available


Publication for CGHcall

CGHcall citations


Xome Blender: A novel cancer genome simulator

PLoS One
PMCID: 5886411
PMID: 29621252
DOI: 10.1371/journal.pone.0194472

[…] er for regions of germline copy number variation. The results are provided in tab-separated format. The third function is optional and allows segmentation using CBS [] as implemented in the R-package CGHcall 2.22.0 [], and plotting of the results. Control-FREEC takes as an input aligned reads, then constructs and normalizes the copy number profile, constructs the BAF profile, segments both profile […]


Drosophila Larval Brain Neoplasms Present Tumour Type Dependent Genome Instability

PMCID: 5873911
PMID: 29467187
DOI: 10.1534/g3.117.300489

[…] using the function “normalize.quantiles” from the “preprocessCore” R package. Genome segmentation was performed according to () using the “segment” function as implemented in the “DNAcopy” R package “CGHcall”. Segmentation and all subsequent steps were performed for each tumor type independently. For each comparison of interest, the ratio was computed between the sample and its corresponding contr […]


High STAP1 expression in DUX4 rearranged cases is not suitable as therapeutic target in pediatric B cell precursor acute lymphoblastic leukemia

Sci Rep
PMCID: 5766593
PMID: 29330417
DOI: 10.1038/s41598-017-17704-4

[…] and 1 μg reference genomic DNA male pool (G147A, Promega, Leiden, the Netherlands) labeled with ULS-Cy3 (Agilent Genomic DNA ULS Labeling Kit). Using median log ratios, data were normalized using the CGHcall version 2.14.0, centralized using CGHnormaliter version 1.8.0, and segmented and called using CGHcall default settings (−1 for loss, 0 for diploid, 1 for gain and 2 for amplification) in R ver […]


Differentially expressed microRNAs in lung adenocarcinoma invert effects of copy number aberrations of prognostic genes

PMCID: 5823624
PMID: 29507679
DOI: 10.18632/oncotarget.24070

[…] LUAD tumor samples (see Table ). Each of the public datasets was first normalized, segmented and additionally underwent post-segmentation normalization using methods provided by Bioconductor package CGHcall (v2.22.0) []. All three datasets then underwent a “calling” process using the CGHcall method from the same package, converting the continuous log-ratios on each probe, to one of the three disc […]


Integrative analysis of genome wide gene copy number changes and gene expression in non small cell lung cancer

PLoS One
PMCID: 5675410
PMID: 29112949
DOI: 10.1371/journal.pone.0187246

[…] n were assigned to each of the 261801 SNPs using a two-level hierarchical mixture model which utilizes the breakpoint information from the CBS []. CN frequency plots were created using the R package ‘CGHcall’ [], plotting the percentage of patients with a particular aberration (CN gain, high gain, CN loss, homozygous deletion) across chromosomal positions.Modified Manhattan plots based on the func […]


Association Of Plasma And Urinary Mutant DNA With Clinical Outcomes In Muscle Invasive Bladder Cancer

Sci Rep
PMCID: 5514073
PMID: 28717136
DOI: 10.1038/s41598-017-05623-3

[…] excluded from downstream analysis. Within the QDNAseq package, bins were segmented using the ‘Circular Binary Segmentation’ algorithm and significantly ‘amplified’ or ‘lost’ regions were called using CGHcall – regions were called in peripheral fluids independent of the calls from the corresponding TUR sample.We compared overall levels of copy number imbalance across the length of the genome in our […]


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CGHcall institution(s)
Department of Pathology, VU University Medical Center, Amsterdam, Netherlands

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