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HaarSeg specifications

Information


Unique identifier OMICS_02574
Name HaarSeg
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C, C++, R
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for HaarSeg

HaarSeg in publications

 (6)
PMCID: 3848591
PMID: 24034811
DOI: 10.1186/1868-7083-5-16

[…] snp array 6.0 annotations release 29, july 2009) and on x and y chromosomes were removed. autosomal log2 ratios were centred to a median of zero and segmented using glad (hupe et al., 2004) with the haarseg algorithm []. as described previously [], gistic analysis [] was performed to identify regions of significant copy number gain and loss using the genepattern public server [] with the default […]

PMCID: 3681672
PMID: 23785299
DOI: 10.1371/journal.pgen.1003553

[…] baf of be sample, (mbaf = abs (baf of be sample – 0.5)*2) for heterozygous (informative for loh) snps only. we performed separate wavelet-based segmentation on these three signal profiles using the haarseg algorithm from the glad package (using parameters haarstart = 3, haarend = 9, fdrq = 0.0001, onlysmoothing = t)., for each individual, we combined all break points of the segmented three […]

PMCID: 3712326
PMID: 23697330
DOI: 10.1186/1471-2105-14-164

[…] bioconductor to fit the glad adaptive weights smoothing model []. we varied the degree of smoothness by adjusting the lambdabreak and minbkpweight parameters of the daglad function. for the glad.haarseg model, we used the smoothfunc=~haarseg~ option and varied the breaksfdrq parameter to fit a wavelet smoothing model []., to fit a gaussian maximum-likelihood piecewise constant smoothing […]

PMCID: 3500050
PMID: 23173005
DOI: 10.1371/journal.pgen.1003027

[…] isolated from tumors, fluorescently labeled, and competitively hybridized with wt dna spotted bac (bacterial artificial chromosomes) arrays. all data were submitted to geo (gse40925). we used the haarseg algorithm with default parameters implemented in wavicgh (wavi.bioinfo.cnio.es) for chromosomal segmentation of mutations and for cna calling. we manually curated bac clones spanning putative […]

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

[…] we compare our newly developed method to several existing normalization methods (global loess, poplowess, and cghnormaliter) as well as to the methods combining normalization and segmentation (haarseg, genome alteration detection analysis (gada), and circular binary segmentation (cbs) combined normalization) [,,]. the significant performance improvement of our channel-specific […]


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HaarSeg institution(s)
Department of Electrical Engineering, Technion-Israel Institute of Technology, Haifa Israel

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