aCGH.Spline statistics

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aCGH.Spline specifications

Information


Unique identifier OMICS_02607
Name aCGH.Spline
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 2.2
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Tomas W. Fitzgerald <>

Publication for aCGH.Spline

aCGH.Spline in publications

 (3)
PMCID: 3751642
PMID: 23763846
DOI: 10.1186/1471-2164-14-398

[…] the reference sample with cy3 and cy5. fluorescence intensities ratios were extracted using agilent feature extraction software (agilent technologies). log2ratio profiles were then normalized using acgh-spline to remove dye biases and reduce experimental noise []. cnv detection was performed using a modified version of cnvfinder [], where we optimized empirically significance thresholds using […]

PMCID: 3626651
PMID: 23596509
DOI: 10.1371/journal.pone.0060482

[…] scanned image using feature extraction software version 10.5.1.1., the two fluorescence intensity distributions were then adjusted independently towards their geometric mean using the r package “acgh.spline”. this method used a cubic spline interpolation and outlier extrapolation to account for non-standard dye biases (the experimental design results in a large dye bias and number […]

PMCID: 3239208
PMID: 21948799
DOI: 10.1093/nar/gkr764

[…] the gain of an extra copy. the raw array data was normalized using a robust cubic spline interpolation method contained inside the r® package acgh. spline (http://cran.r-project.org/web/packages/acgh.spline/index.html) to adjust for dye biases. a custom wavelet transform was applied to remove the presence of genomic waves and the true baseline was estimated using the median value reported […]


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aCGH.Spline institution(s)
Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK; Bioinformatics Group, Cranfield University, Cranfield, Bedfordshire, UK; Inserm UMR915, l'Institut du Thorax and Centre Hospitalier Universitaire (CHU), Nantes, France
aCGH.Spline funding source(s)
This work was supported by the Wellcome Trust (grant number WT077008).

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