CNAseg statistics

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Citations per year

Number of citations per year for the bioinformatics software tool CNAseg

Tool usage distribution map

This map represents all the scientific publications referring to CNAseg per scientific context
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CNAseg specifications


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 citations


A Total variation Constrained Permutation Model for Revealing Common Copy Number Patterns

Sci Rep
PMCID: 5575355
PMID: 28851906
DOI: 10.1038/s41598-017-09139-8

[…] rator (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 tha […]


Copy number alterations detected by whole exome and whole genome sequencing of esophageal adenocarcinoma

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

[…] ese 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 work […]


Detection of Genomic Structural Variants from Next Generation Sequencing Data

Front Bioeng Biotechnol
PMCID: 4479793
PMID: 26161383
DOI: 10.3389/fbioe.2015.00092

[…] e for 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., ). Recent […]


PSCC: Sensitive and Reliable Population Scale Copy Number Variation Detection Method Based on Low Coverage Sequencing

PLoS One
PMCID: 3897425
PMID: 24465483
DOI: 10.1371/journal.pone.0085096

[…] d in tumor samples , . The read counts method can achieve a high resolution in a relatively low coverage sequencing, and some recently popular algorithms are based on it, including SegSeq , CNV-seq , CNAseg , ReadDepth and rSW-seq . However, most of these algorithms need one real or theoretical comparative genome, which induce an additional cost or unexpected fluctuations that prevent further lar […]


Computational tools for copy number variation (CNV) detection using next generation sequencing data: features and perspectives

BMC Bioinformatics
PMCID: 3846878
PMID: 24564169
DOI: 10.1186/1471-2105-14-S11-S1

[…] bias can be effectively cancelled out by comparing the paired genomes directly at each region [,,], thereby taking advantage of the similarity of GC bias between the two paired samples. For instance, CNAseg implemented an algorithm locally weighted scatterplot smoothing (LOWESS) regression to adjust the GC bias for matched samples in each 10-Kb window. Moreover, Discrete Wavelet Transform (DWT) is […]

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

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