CGHseg specifications

Information


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
Requirements
methods, parallel
Maintained Yes

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Publication for CGHseg

CGHseg in publications

 (18)
PMCID: 4760083
PMID: 26613787
DOI: 10.1093/molbev/msv282

[…] resulted in a mean decrease in variance of probe intensity of 24.3% (range 0.75–53.5%). using this final probe set of 188,081 probes, we segmented the genome into regions of common intensity using cghseg. this probe set covers 5,148 genes, accounting for 11.6 mb of the p. falciparum genome., to identify appropriate thresholds for determining segments that exhibit cnv, we sequenced four […]

PMCID: 4622673
PMID: 26237076
DOI: 10.1080/15592294.2015.1062207

[…] 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 […]

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

[…] 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 […]

PMCID: 4364008
PMID: 25780929
DOI: 10.1371/journal.pone.0118865

[…] 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 (http://compbio.med.harvard.edu/cghweb). as p. falciparum is a haploid organism, relatively low single value cutoffs of log2ratio of normalized cy5/cy3 values, 0.5 […]

PMCID: 4159007
PMID: 25062919
DOI: 10.1093/gbe/evu158

[…] 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 […]


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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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