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chevron_left CNV detection Tumor purity and heterogeneity estimation chevron_right
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Protocols

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

Versioning


No version available

Maintainer


  • person_outline Stefano Berri

Publication for CNAnorm

CNAnorm citations

 (11)
library_books

Adaptive Mistranslation Accelerates the Evolution of Fluconazole Resistance and Induces Major Genomic and Gene Expression Alterations in Candida albicans

2017
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., […]

library_books

The genomic road to invasion—examining the similarities and differences in the genomes of associated oral pre cancer and cancer samples

2017
Genome Med
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 […]

library_books

Establishment of a novel cellular model for myxofibrosarcoma heterogeneity

2017
Sci Rep
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 […]

library_books

Genomic profiling of multiple sequentially acquired tumor metastatic sites from an “exceptional responder” lung adenocarcinoma patient reveals extensive genomic heterogeneity and novel somatic variants driving treatment response

2016
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. […]

library_books

Polycomb Repressor Complex 1 Member, BMI1 Contributes to Urothelial Tumorigenesis through p16 Independent Mechanisms1

2015
Transl Oncol
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 […]

library_books

Whole genome sequencing provides new insights into the clonal architecture of Barrett’s esophagus and esophageal adenocarcinoma

2015
Nat Genet
PMCID: 4556068
PMID: 26192915
DOI: 10.1038/ng.3357

[…] were compared with the expected ones for each copy number, purity and ploidy combination to identify the model with the smallest least-squares value. since this method is unpublished we also ran cnanorm for case p12 eac and demonstrated the same results., in order to assess any clonal heterogeneity within patient ahm1051’s barrett’s esophagus segment, snvs with the highest variant allele […]


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

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