CGHnormaliter protocols

View CGHnormaliter computational protocol

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CGHnormaliter specifications

Information


Unique identifier OMICS_02572
Name CGHnormaliter
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 1.34.0
Stability Stable
Requirements
methods, stats, Biobase, utils, CGHbase, CGHcall(>=2.17.0), CGHbase(>=1.15.0), CGHcall
Maintained Yes

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Maintainer


  • person_outline Bart van Houte <>

Publications for CGHnormaliter

CGHnormaliter in pipeline

2018
PMCID: 5766593
PMID: 29330417
DOI: 10.1038/s41598-017-17704-4

[…] in gc content of dna fragments, the r package arraytv version 1.12.0 was used. to compare the logr values of the copy numbers between samples a centralization step was performed, using the r package cghnormaliter version 1.28.0. data were called using cghcall version 2.36.0 default settings (−2 for double loss, −1 for loss, 0 for diploid, 1 for gain and 2 for amplification) in r version 3.3.3., […]


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CGHnormaliter in publications

 (5)
PMCID: 5766593
PMID: 29330417
DOI: 10.1038/s41598-017-17704-4

[…] 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 version 2.14.1., to identify whether copy […]

PMCID: 5354859
PMID: 27894077
DOI: 10.18632/oncotarget.13492

[…] the netherlands) labeled with uls-cy3 (agilent genomic dna uls labeling kit). copy number microarray data were normalized using median log ratio in 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 version 2.14.1., the salsa p335 all-ikzf1 […]

PMCID: 4566396
PMID: 26358114
DOI: 10.1186/s12920-015-0132-y

[…] for the agilent platforms, we first performed a check of the quality control (qc) results, discarding those probes associated with a poor qc value. for the normalization of all of the data, we used cghnormaliter []. each input file (sample) has a corresponding normalized output containing information on the call, segmentation and normalized log-ratio of all 22 autosomes. as the output, […]

PMCID: 3556652
PMID: 23046790
DOI: 10.1186/gm377

[…] gc content. these were selected after investigating dependence of log ratio on multiple factors, including gc content in windows of up to 500 kb centered around each probe. the bioconductor package cghnormaliter [] was then used to correct for intensity dependence and log2 ratios scaled to be comparable between arrays using the 'scale' method in the package limma []. replicate arrays […]

PMCID: 3245619
PMID: 21854607
DOI: 10.1186/gb-2011-12-8-r80

[…] reference samples on intensities using all probes []. the snapcgh package commonly used for analyzing array cgh data has included the global loess normalization method []. furthermore, poplowess and cghnormaliter have been developed for array cgh data [,]. poplowess attempts to separate normal from aberrant probes using k-means clustering and applies the loess normalization based on the largest […]


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CGHnormaliter institution(s)
Centre for Integrative Bioinformatics VU, VU University Amsterdam, De Boelelaan, Netherlands
CGHnormaliter funding source(s)
Supported by Netherlands Genomics Initiative (HH: NGI/Centre for Medical Systems Biology, BvH: NGI/Ecogenomics); Netherlands Bioinformatics Centre (TB: NBIC/BioRange).

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