quantsmooth specifications

Information


Unique identifier OMICS_02067
Name quantsmooth
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 1.46.0
Stability Stable
Requirements
R(>=2.10.0), grid, quantreg
Maintained Yes

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Publication for quantsmooth

quantsmooth in publications

 (6)
PMCID: 5438707
PMID: 28423671
DOI: 10.18632/oncotarget.15993

[…] an association was considered as significant if bonferroni corrected p-value was less than 0.05. genome wide correlation between dna methylation and gene expression was visualized using r package, quantsmooth []., the median methylation of cpgs in the region of ‘gene region collapsed’ and gene expression of corresponding gene was tested for non-zero correlation using person correlation (r […]

PMCID: 5325768
PMID: 28092684
DOI: 10.1038/ng.3762

[…] were tested by sanger sequencing for segregation with disease. sequence data were analyzed with sequencer 4.9 (gene codes)., chromosomal ideogram plot were generated using the bioconductor package quantsmooth. red: homozygous regions that segregate between affected and unaffected family members., fibroblasts were generated from unaffected and affected dermal biopsies explants. ipscs, neural […]

PMCID: 4165906
PMID: 25146004
DOI: 10.1186/s13059-014-0435-x

[…] an association was considered significant if the bonferroni corrected p-value was smaller than 0.05. genome-wide correlation between methylation and expression was visualized using the r package quantsmooth []. second, the median methylation level of cpgs in the 'gene region collapsed' data and gene expression of the corresponding gene was tested for non-zero correlation using pearson […]

PMCID: 3227572
PMID: 22140428
DOI: 10.1371/journal.pone.0026362

[…] at a distinct dna sequence. from single cell analysis of mda-mb-468 cells displaying different egfr copy numbers, the precise amplicon borders were calculated by the smoothing function of the quantsmooth algorithm . a further extension of the amplicon was found in mda-mb-468 cells with the highest copy number gain (32 copies), showing an additional sequence extension on the centromeric […]

PMCID: 2728899
PMID: 19696946
DOI: 10.1155/2009/201325

[…] and particularly to apply a new normalization algorithm to correct for local spatial bias and continuous spatial gradients []. two methods were available for smoothing array-cgh data, namely, quantsmooth, using a quantile smoothing method [] and waveslim, which is part of the r project, using smoothing algorithm denoising by wavelets []. segmentation or breakpoint detection methods detect […]


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quantsmooth institution(s)
Department of Medical Statistics, Leiden University Medical Centre, RC, Leiden, Netherlands

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