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Protocols

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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Versioning


No version available

Documentation


Maintainer


  • person_outline Bart van Houte

Publications for CGHnormaliter

CGHnormaliter citations

 (5)
library_books

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

2018
Sci Rep
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 […]

library_books

Tyrosine kinase fusion genes in pediatric BCR ABL1 like acute lymphoblastic leukemia

2016
Oncotarget
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 […]

library_books

Genome instability model of metastatic neuroblastoma tumorigenesis by a dictionary learning algorithm

2015
BMC Med Genomics
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, […]

library_books

Digital transcriptome profiling of normal and glioblastoma derived neural stem cells identifies genes associated with patient survival

2012
Genome Med
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 […]

library_books

Single cell copy number variation detection

2011
Genome Biol
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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