CNAseg specifications

Information


Unique identifier OMICS_00337
Name CNAseg
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Input format BAM
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Stability No
Maintained No

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Publication for CNAseg

CNAseg in publications

 (5)
PMCID: 5575355
PMID: 28851906
DOI: 10.1038/s41598-017-09139-8

[…] (lasso) regression to identify the breakpoint and detects copy number profiles. cnv-seq (copy number variation using shotgun sequencing) uses a gaussian distribution to model read depth signal. cnaseg (copy number abnormality segmentation) employs a hidden markov model(hmm) and pearson’s χ 2 statistic to segment read depth signal and get the copy number profile. recent studies have shown […]

PMCID: 4570720
PMID: 26374103
DOI: 10.1186/s40246-015-0044-0

[…] methods can be further categorized according to the study design. some commonly used ones are as follows. (a) cnvnator [], rdxplorer [], and readdepth [] detect cnas on a single tumor sample. (b) cnaseg [], segseq [], exomecnv [], hmmcopy [], and varscan2 [] identify cnas on matched tumor-normal samples. control-freec [, ] can be categorized both into classes (a) and (b), as it can either […]

PMCID: 4479793
PMID: 26161383
DOI: 10.3389/fbioe.2015.00092

[…] the regions of the same length., a considerable number of methods for the detection of cnv in whole-genome sequencing (wgs) data have been reported in the literature, including cnvnator, cnanorm, cnaseg, rsw-seq, cn.mops, jointslm, readdepth, and bic-seq (ivakhno et al., ; kim et al., ; abyzov et al., ; magi et al., ; miller et al., ; xi et al., ; gusnanto et al., ; klambauer et al., ). […]

PMCID: 3902584
PMID: 24478987
DOI: 10.3389/fonc.2014.00007

[…] in cells having an abnormal number of copies of one or more sections of dna. currently many software packages are available for calling cnvs in bulk dna sequencing, such as cnv-seq (), pencnv (), cnaseg (), readdepth (), and cn.mops (). however, few software packages and algorithms have been designed for single cell cnv calling, and the impact of amplification bias on cnv calling […]

PMCID: 3604020
PMID: 23527109
DOI: 10.1371/journal.pone.0059128

[…] of the existing cnv detection methods to the best of the authors’ knowledge. rsw-seq was excluded because of no publicly available codes. cnanorm was not available when we started our study. cnd and cnaseg were excluded because of stability issue. from the same dataset, there were issues getting the code to fully perform to our expectations. our study focused on the method with doc signature, […]


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CNAseg institution(s)
Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Cambridge, UK

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