SynthEx specifications

Information


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

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Versioning


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Documentation


Maintainer


  • person_outline Mengjie Chen

Publication for SynthEx

SynthEx citations

 (2)
library_books

Single Cell Genomic Analysis in Plants

2018
Genes
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 […]

library_books

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

2017
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 All statistical analyses were performed in R using standard implementation.We analysed copy number using SynthEx (unpublished, http://chenmengjie.github.io/SynthEx). 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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