CNAnorm protocols

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CNAnorm specifications

Information


Unique identifier OMICS_00336
Name CNAnorm
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format BAM
Biological technology Illumina
Operating system Unix/Linux, Mac OS, Windows
Programming languages Perl, R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.12.0
Stability Stable
Requirements
methods
Maintained Yes

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Maintainer


  • person_outline Stefano Berri <>

Publication for CNAnorm

CNAnorm in pipelines

 (2)
2017
PMCID: 5461742
PMID: 28592326
DOI: 10.1186/s13073-017-0442-0

[…] and sequenced together in one 2 × 100 bp illumina hiseq2500 lane, giving around 0.15× coverage per sample., sequencing reads were trimmed using cutadapt []. genomic copy number data were produced by cnanorm [] after first aligning to the human reference genome (hg19) using bwa []. breakpoints were called using dnacopy []. human papilloma virus (hpv) infection was tested by re-aligning the data […]

2015
PMCID: 4631094
PMID: 26500029
DOI: 10.1016/j.tranon.2015.08.002

[…] . copy number was calculated by splitting the genome into equal-sized windows with an average of 400 reads per window and comparing ratio of tumor and normal samples, and plots were produced using cnanorm with breakpoints called using dnacopy . nhuc-bmi1 samples were compared with isogenic mock or vector transduced cells., gene expression analysis was performed using affymetrix hg_u133 plus […]

CNAnorm in publications

 (11)
PMCID: 5549176
PMID: 28808688
DOI: 10.1128/mSphere.00167-17

[…] loh of bases with different genotype compared with the control strain. structural variations in coding regions were also analyzed for changes in codon usage., copy number analysis was performed with cnanorm (). aligned reads of each sample were split into 2-kb windows, and reads were counted. cnanorm was used to estimate copy numbers with normalization of paired control and test samples., […]

PMCID: 5461742
PMID: 28592326
DOI: 10.1186/s13073-017-0442-0

[…] and sequenced together in one 2 × 100 bp illumina hiseq2500 lane, giving around 0.15× coverage per sample., sequencing reads were trimmed using cutadapt []. genomic copy number data were produced by cnanorm [] after first aligning to the human reference genome (hg19) using bwa []. breakpoints were called using dnacopy []. human papilloma virus (hpv) infection was tested by re-aligning the data […]

PMCID: 5356330
PMID: 28304377
DOI: 10.1038/srep44700

[…] library kit (cat.nr. 4471252, thermo fisher scientific). dna libraries were sequenced on the ion proton sequencer yielding 8–10 million reads per library. cnv analysis was performed using the cnanorm bioconductor r package. briefly, reads were aligned to hg19 and summarized in windows of 10 kb size. cnanorm was used to normalize for gc content and perform cnv analysis using coverage data […]

PMCID: 5111000
PMID: 27900369
DOI: 10.1101/mcs.a001263

[…] (>33%) of the loh snvs and indels were found in these cnv regions (supplemental tables s7a,b). because this heterogeneity could be due to disparity in tumor content between the two sites, we used cnanorm () to determine tumor content. however, we found that the tumor content in the lung tumor was ∼56%, whereas the tumor content in the metastatic lymph node was nearly 32% (supplemental fig. […]

PMCID: 4631094
PMID: 26500029
DOI: 10.1016/j.tranon.2015.08.002

[…] . copy number was calculated by splitting the genome into equal-sized windows with an average of 400 reads per window and comparing ratio of tumor and normal samples, and plots were produced using cnanorm with breakpoints called using dnacopy . nhuc-bmi1 samples were compared with isogenic mock or vector transduced cells., gene expression analysis was performed using affymetrix hg_u133 plus […]

CNAnorm institution(s)
Department of Statistics, University of Leeds, Leeds, UK

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