SynthEx specifications


Unique identifier OMICS_22174
Name SynthEx
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License MIT License
Computer skills Advanced
Stability Stable
Maintained Yes




No version available



  • person_outline Mengjie Chen

Publication for SynthEx

SynthEx citations


Single Cell Genomic Analysis in Plants

PMCID: 5793201
PMID: 29361790
DOI: 10.3390/genes9010050

[…] ntent, variant position, and repeat sequences []. This additional information can be incorporated into novel CNV identification algorithms, which combine a synthetic-normal-based DNA sequencing tool (SynthEx) with allele-specific copy number analysis (ASCN) [], to address amplification bias and reduce unexpected variations in single-cell sequencing data []. Other newly developed single-cell CNV de […]


Genomic analysis of oesophageal squamous cell carcinoma identifies alcohol drinking related mutation signature and genomic alterations

Nat Commun
PMCID: 5477513
PMID: 28548104
DOI: 10.1038/ncomms15290

[…] s were considered significant. Mutual exclusive analysis was performed using gitools (v2.2.2). All statistical analyses were performed in R using standard implementation.We analysed copy number using SynthEx (unpublished, In brief, 100 kb bin counts data (segment data) were generated using BEDTools. The read ratios were calculated using the ‘synthetic normal' […]

SynthEx institution(s)
Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, NC, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA; Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL, USA; Public Health Division, Fred Hutchison Cancer Research Center, Seattle, WA, USA
SynthEx funding source(s)
Supported by funds from the National Cancer Institute (NCI) Breast SPORE program grant P50-CA58223-09A1, NCI RO1-CA148761, the Breast Cancer Research Foundation, and NCI F30- CA200345-01; by the National Institutes of Health (NIH) grants R01 CA082659 and P01 CA142538.

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