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CGHseg specifications


Unique identifier OMICS_00712
Name CGHseg
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 1.0.2
Stability Stable
methods, parallel
Maintained Yes


No version available

Publication for CGHseg

CGHseg citations


Population Structure Shapes Copy Number Variation in Malaria Parasites

Mol Biol Evol
PMCID: 4760083
PMID: 26613787
DOI: 10.1093/molbev/msv282

[…] frequency of < 5%. The accuracy of SNP typing for this platform have been previously tested (Tan et al. ; Cheeseman et al. ; Manske et al. ). CNV calling was performed by segmenting the genome using CGHseg using default settings and classifying gains and losses as regions which had >8 probes and had a log 2 ratio (cy3/cy5) > 2.5 (for amplifications) or 3 (for deletions) times the standard deviati […]


Environmentally induced epigenetic transgenerational inheritance of sperm epimutations promote genetic mutations

PMCID: 4622673
PMID: 26237076
DOI: 10.1080/15592294.2015.1062207

[…] ormed as previously described. For the CGH, following normalization, the average value of each probe was calculated and 2 different copy number variation algorithms were used on each of these probes: CGHseg and cghFlasso. These 2 algorithms were used with the default parameters. Average values from the output of these algorithms were obtained. A threshold of 0.05 as a cut-off was used on the summ […]


Robust BRCA1‐like classification of copy number profiles of samples repeated across different datasets and platforms

Mol Oncol
PMCID: 5528812
PMID: 25825120
DOI: 10.1016/j.molonc.2015.03.002

[…] values that fall within the chromosomal start and end position of the BAC clones (). We used custom functions using the functionality from the following R packages in the mapping process: DNAcopy (), cghseg (), Genomic Ranges (), KCsmart () and, copy number (). The median BAC size was approximately 150 kb and the median number of probes averaged 3 for BAC32K (range 1–12), 6 for NG135 (range 1–30), […]


Functional Analysis of Sirtuin Genes in Multiple Plasmodium falciparum Strains

PLoS One
PMCID: 4364008
PMID: 25780929
DOI: 10.1371/journal.pone.0118865
call_split See protocol

[…] reference genome (PlasmoDB v5.4) and non-unique probes were discarded. A total of 383,333 probes were used for CNV analysis. Segmentation analysis for identification of CNV regions was performed with CGHSeg algorithm [] using CGHweb ( As P. falciparum is a haploid organism, relatively low single value cutoffs of log2ratio of normalized Cy5/Cy3 values, 0.5 and […]


MPAgenomics: an R package for multi patient analysis of genomic markers

BMC Bioinformatics
PMCID: 4269855
PMID: 25495450
DOI: 10.1186/s12859-014-0394-y

[…] f diseases, e.g. cancer, on the human genome.Analyzing data from genome-wide SNP arrays within R requires several packages, e.g. aroma for normalization of Affymetrix®; SNP arrays [,], changepoint or cghseg for segmentation of copy number profiles [], cghcall for labelling segments [], and glmnet for penalized regressions []. Each package performs a specific task along the whole analysis but none […]


Epigenetics and the Evolution of Darwin’s Finches

Genome Biol Evol
PMCID: 4159007
PMID: 25062919
DOI: 10.1093/gbe/evu158
call_split See protocol

[…] llowing normalization, the average value of each probe was calculated and three different CNV algorithms were used on each of these probes including circular binary segmentation from the DNA copy (), CGHseg () and cghFlasso (). These three algorithms were used with the default parameters. The average values from the output of these algorithms were obtained. A threshold of 0.04 as a cutoff was used […]


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CGHseg institution(s)
Laboratoire de Biometrie et Biologie Evolutive, UMR CNRS 5558 - Univ Lyon, Villeurbanne, France; Projet BAMBOO, INRIA Rhône-Alpes, Montbonnot Saint-Martin, France
CGHseg funding source(s)
Institut National du Cancer (INCA)

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