regSNPs specifications

Information


Unique identifier OMICS_11183
Name regSNPs
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Yunlong Liu <>

Publication for regSNPs

regSNPs in publications

 (3)
PMCID: 5613474
PMID: 28950915
DOI: 10.1186/s13059-017-1320-1

[…] sites on thousands of messenger rnas., synonymous single-nucleotide variants (ssnvs) are usually left out of analyses because of the absence of resulting amino acid changes. however, by using regsnps-splicing software to prioritize ssnvs associated with rna splicing, yunlong liu (indiana university, usa) found that disease-causing ssnvs are enriched in protein functional domains. […]

PMCID: 5154163
PMID: 27964748
DOI: 10.1186/s13073-016-0382-0

[…] strength of binding; however, recent studies have examined the actual sequences themselves, to identify variants that affect dna binding. bcrank is an algorithm designed to detect regulatory snps (regsnps) in chip-chip data based upon snp genotyping in dna-binding sites []. more recently, another strategy used chip-seq data to nominate regsnps using the assumption that the enrichment of snps […]

PMCID: 3483423
PMID: 23001124
DOI: 10.1038/ng.2416

[…] map to transcription factor binding sites or histone modifications favorable to binding. these represent the regulatory regions where binding sites can be created or destroyed; we refer to these as regsnps, which are processed in a similar manner to ldsnps. we then calculate the modulator quotient. the numerator of this quotient is the number of rasnp/regsnp clusters that have at least one […]


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regSNPs institution(s)
School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China; Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA; Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, UK; Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA
regSNPs funding source(s)
National Institutes of Health grants AA017941 and AG041517

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