tQN protocols

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tQN specifications

Information


Unique identifier OMICS_02605
Name tQN
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for tQN

tQN in pipeline

2016
PMCID: 4947184
PMID: 27406316
DOI: 10.1038/ncomms12222

[…] genes., illumina omni1 quad and omniexpress snp arrays quality control and normalization was performed using genomestudio genotyping module. a supplementary normalization step was applied using the tqn algorithm. allelic cnvs were analysed using gap and ascat 2.0 (ref. ). tumour purity was estimated using both approaches, with a good correlation, although gap estimates were found to be always […]


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tQN in publications

 (12)
PMCID: 5958058
PMID: 29773832
DOI: 10.1038/s41467-018-04383-6

[…] raw fluorescent signals and to obtain log r ratio (lrr) and b allele frequency (baf) values. asymmetry in baf signals due to bias between the two dyes used in illumina assays was corrected using the tqn normalization procedure. we used the circular binary segmentation algorithm to segment genomic profiles and assign corresponding smoothed values of lrr and baf. the genome alteration print method […]

PMCID: 4947184
PMID: 27406316
DOI: 10.1038/ncomms12222

[…] genes., illumina omni1 quad and omniexpress snp arrays quality control and normalization was performed using genomestudio genotyping module. a supplementary normalization step was applied using the tqn algorithm. allelic cnvs were analysed using gap and ascat 2.0 (ref. ). tumour purity was estimated using both approaches, with a good correlation, although gap estimates were found to be always […]

PMCID: 4838899
PMID: 27090007
DOI: 10.1038/ncomms11263

[…] raw fluorescent signals and to obtain log r ratio (lrr) and b allele frequency (baf) values. asymmetry in baf signals due to bias between the two dyes used in illumina assays was corrected using the tqn normalization procedure. we used the circular binary segmentation algorithm to segment genomic profiles and assign corresponding smoothed values of log r ratio and b allele frequency. the genome […]

PMCID: 4621769
PMID: 26400872
DOI: 10.1530/ERC-15-0086

[…] genome studio software (). this affected both the allelic proportions and the copy number estimates. data were corrected for this bias using a quantile normalization approach implemented in the tqn method (). bias in the estimated copy number related to gc binding artifacts was corrected for using the method by (). allele specific copy number estimates corrected for ploidy and infiltration […]

PMCID: 4534696
PMID: 26288838
DOI: 10.1016/j.ebiom.2015.06.022

[…] (). obtained fdr-adjusted two-sided p-values¬†<¬†0.05 were considered significant., copy number estimates and allelic intensity ratios exported by illumina beadstudio were normalized with tqn-procedure (). subsequently, log2-r-ratios (lrr) were calculated from normalized copy number estimates of the tumors and matched blood samples. for tumors with no matching blood sample, […]


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tQN institution(s)
Department of Oncology, Clinical Sciences, Lund University, Lund, Sweden

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