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GenoCN specifications

Information


Unique identifier OMICS_02567
Name GenoCN
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Mac OS, Windows
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for GenoCN

GenoCN citations

 (6)
call_split

Metabolic characterization of isocitrate dehydrogenase (IDH) mutant and IDH wildtype gliomaspheres uncovers cell type specific vulnerabilities

2018
PMCID: 5905129
PMID: 29692895
DOI: 10.1186/s40170-018-0177-4
call_split See protocol

[…] io (LRR) values. Secondly, we used the PennCNV software (parameters: exome HMM model with gcmodel adjustment, filtered by 10 SNPs minimum 10 and with region length longer than 50 k) [], the R package GenoCN (parameters: cnv-only snpInfo$PFB > 1; outputSNP 1; outputSeg TRUE) [], and the R package Rawcopy (default parameters) [] for CNV inference. CNV calls were obtained by integrating the output fr […]

library_books

TP53 mutations, tetraploidy and homologous recombination repair defects in early stage high grade serous ovarian cancer

2015
Nucleic Acids Res
PMCID: 4538798
PMID: 25916844
DOI: 10.1093/nar/gkv111

[…] lumina 650 genotyping array data were used. We used the paired option in Illumina GenomeStudio and extracted the log relative ratio (LRR) and the B-allele frequency of the germline and tumor DNA. The genoCN () R package was used to detect somatic CN alterations (CNAs) requiring a minimum of 20 probes per CNA interval. The genoCNA function also estimates computationally the tumor purity, defined as […]

library_books

Hidden Markov Model Based CNV Detection Algorithms for Illumina Genotyping Microarrays

2015
Cancer Inform
PMCID: 4310714
PMID: 25657572
DOI: 10.4137/CIN.S16345

[…] fied by PennCNV overlap with both QuantiSNP and GenoCN, and only a limited amount of unique CNV regions are identified by PennCNV. In contrast, the majority of CNV regions identified by QuantiSNP and GenoCN in the HapMap samples are unique to the algorithm. The distribution of CNV size for each sample, in terms of kilobases and also with regard to the number of probes on the genotyping array, was […]

library_books

Identification of Allelic Imbalance with a Statistical Model for Subtle Genomic Mosaicism

2014
PLoS Comput Biol
PMCID: 4148184
PMID: 25166618
DOI: 10.1371/journal.pcbi.1003765

[…] his BAF pattern are use of a two-component mixture distribution and mirroring.In one approach, the observed data are modeled as a two-component mixture. We discuss and evaluate two such methods here. genoCN , a discrete-state hidden Markov model (HMM) based method, uses the BAFs at germline heterozygous sites as the observed data and defines the emission function as a mixture of the distribution f […]

library_books

HaplotypeCN: Copy Number Haplotype Inference with Hidden Markov Model and Localized Haplotype Clustering

2014
PLoS One
PMCID: 4029584
PMID: 24849202
DOI: 10.1371/journal.pone.0096841

[…] ree algorithms account for the distance between neighboring loci; the longer the distance between any two loci, the more likely a state change will occur between them. QuantiSNP, PennCNV, PICNIC, and GenoCN can provide allele-specific copy numbers (ASCN), and cnvHap can further provide haplotypes composed of allelic copy number change on the same chromosomes. However, the copy numbers are pre-spec […]

library_books

Sensitive and specific detection of mosaic chromosomal abnormalities using the Parent of Origin based Detection (POD) method

2013
BMC Genomics
PMCID: 3680018
PMID: 23724825
DOI: 10.1186/1471-2164-14-367

[…] sed CNV detection tool which is capable of improved detection using parent–child trios, but is not designed to detect UPD or partial copy number states []. Other HMM-based approaches, including PSCN, genoCN, MixHMM, and GPHMM, can detect CNVs and UPD events in tumor/normal mixtures and are thus capable of detecting mosaic changes at a certain level of resolution [-]. A Bayesian-based algorithm, gB […]

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GenoCN institution(s)
Department of Biostatistics, University of North Carolina, Chapel Hill, NC, USA

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