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CODEX specifications

Information


Unique identifier OMICS_07305
Name CODEX
Alternative names COpy number Detection by EXome sequencing, CODEX2
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


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Documentation


Maintainers


  • person_outline Nancy Zhang <>
  • person_outline Yuchao Jiang <>
  • person_outline Yuchao Jiang <>

Additional information


http://www.bioconductor.org/packages/devel/bioc/html/CODEX.html

Publications for COpy number Detection by EXome sequencing

CODEX in pipeline

2016
PMCID: 4902256
PMID: 27285585
DOI: 10.1371/journal.pone.0157125

[…] ]. after down-sampling by gatk, a mean target coverage of 197x was achieved. variants were annotated with wannovar []., prediction of copy number variation from sequencing data was performed using codex []. this algorithm normalizes the data using a poisson latent factor model that removes biases due to gc content, exon capture, amplification efficiency, and latent systemic artifacts. six […]


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CODEX in publications

 (5)
PMCID: 5466608
PMID: 28649662
DOI: 10.1038/s41523-017-0024-8

[…] or likely pathogenic mutations (further addressed as “mutations” throughout). in addition, analysis of next generation sequencing (ngs) data by a combination of the exome hidden markov model and copy number detection by exome sequencing algorithms, identified 14 germline copy number variants, 12 of which were classified as likely pathogenic (supplementary table ). therefore, counting single […]

PMCID: 5432334
PMID: 28460482
DOI: 10.18632/oncotarget.15932

[…] technology is essential for the development and application of more precise medical treatments for human cancer. here, we evaluated seven cna estimation tools (exomecnv, conifer, varscan2, codex, ngcgh, saascnv, and falcon) using whole-exome sequencing data from 419 breast cancer tumor-normal sample pairs from the cancer genome atlas. estimations generated using each tool […]

PMCID: 4902256
PMID: 27285585
DOI: 10.1371/journal.pone.0157125

[…] ]. after down-sampling by gatk, a mean target coverage of 197x was achieved. variants were annotated with wannovar []., prediction of copy number variation from sequencing data was performed using codex []. this algorithm normalizes the data using a poisson latent factor model that removes biases due to gc content, exon capture, amplification efficiency, and latent systemic artifacts. six […]

PMCID: 4883269
PMID: 27075447
DOI: 10.1007/s00439-016-1658-6

[…] issues such as poor read mappability, gc bias, and batch effects between sequencing experiments (teo et al. ). many different algorithms have been devised based on read-depth methods, such as codex, convex, conifer, and xhmm (amarasinghe et al. ; fromer et al. ; jiang et al. ; krumm et al. ). comparisons of cnv algorithms for exome data have shown that none of the algorithms performed […]

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

[…] literature for this purpose including exomecnv (sathirapongsasuti et al., ), conifer (krumm et al., ), cnv-seq (xie and tammi, ), xhmm (fromer et al., ), and recently excavator (magi et al., ) and codex (jiang et al., ). notably, the method developed by bansal and co-workers (bansal et al., ) allows for the analysis of ngs data generated from small subsets of the exome, namely custom capture […]


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CODEX institution(s)
Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA; Department of Genetics, School of Medicine, University of North Carolina, Chapel Hill, NC, USA; Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Statistics, The Wharton School, University of Pennsylvania, Philadelphia, PA, USA
CODEX funding source(s)
Supported by the National Institutes of Health (NIH) grant R01 HG006137 and P01 CA142538.

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