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Protocols

FunciSNP specifications

Information


Unique identifier OMICS_08577
Name FunciSNP
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
Version 1.24.0
Stability Stable
Requirements
methods, plyr, BiocGenerics, Biobase, IRanges, GenomicRanges, S4Vectors, R(>=2.14.0), ggplot2, scales, snpStats, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, VariantAnnotation, ggplot2(>=0.9.0), FunciSNP.data, Rsamtools(>=1.6.1), rtracklayer(>=1.14.1), ChIPpeakAnno(>=2.2.0), reshape(>=0.8.4)
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Versioning


No version available

Documentation


Maintainer


  • person_outline Simon G. Coetzee <>

Publication for FunciSNP

FunciSNP citations

 (17)
library_books

A catalog of potential putative functional variants in psoriasis genome wide association regions

2018
PMCID: 5929547
PMID: 29715312
DOI: 10.1371/journal.pone.0196635

[…] been shown to play a major role in psoriasis recently []. we queried the biological function for each correlated snp in functional genomic data sets. the analyses were accomplished in r/bioconductor funcisnp package []., we categorized the correlated snps into five groups by the priority of exonic variants, gene promoters, enhancers, transcribed, and repressed regions. coding exon data […]

library_books

Integrative Bioinformatics Approaches for Identification of Drug Targets in Hypertension

2018
PMCID: 5894467
PMID: 29670885
DOI: 10.3389/fcvm.2018.00025

[…] gwas results using bioinformatics tools (–). for instance, fuma provides extensive functional annotation for all snps in associated loci and annotates the identified genes in biological context (). funcisnp investigates functional snps in regulatory regions of interest (). ensemble's variant effect predictor (vep) determines the effect of variants on genes, transcripts, and protein sequence, […]

library_books

Functional annotation of sixty five type 2 diabetes risk SNPs and its application in risk prediction

2017
PMCID: 5337961
PMID: 28262806
DOI: 10.1038/srep43709

[…] coordinates is converted to hg19 by liftover in ucsc., the present work initiates from 65 tag snps. the putative risk snps in linkage disequilibrium with these known risk snps are identified by funcisnp, an r package that allows a population based identification of ld snps from 1,000 genome project. funcisnp had successfully assisted annotation works of risk snps associated with several […]

library_books

GWAS for serum galactose deficient IgA1 implicates critical genes of the O glycosylation pathway

2017
PMCID: 5328405
PMID: 28187132
DOI: 10.1371/journal.pgen.1006609

[…] we examined all of the top most associated variants as well as all snps in ld with the lead snp (r2>0.5) at each locus. we annotated these variants using annovar[], seattleseq[], snpnexus[], funcisnp[], haploreg4[], and chromos[]. the transcripts whose expressions were correlated with the lead snps in cis- or trans- were also identified using available eqtl datasets, including: (1) […]

library_books

Molecular mechanisms underlying noncoding risk variations in psychiatric genetic studies

2017
PMCID: 5378805
PMID: 28044063
DOI: 10.1038/mp.2016.241

[…] of dna elements (encode) and the roadmap epigenomics mapping consortium (remc). these data sets can be routinely mined with multiple computational tools (for example, regulomedb, haploreg, gwava and funcisnp) for the annotation of dna variants., initiated as a follow-up to the human genome project (genomic research), encode project aimed to map the functional elements in the genome, usually […]

library_books

Enrichment of risk SNPs in regulatory regions implicate diverse tissues in Parkinson’s disease etiology

2016
PMCID: 4962314
PMID: 27461410
DOI: 10.1038/srep30509

[…] of most risk snps and an understanding of their biological function in human disease. here, we have addressed this conundrum via the development and use of two bioconductor software tools, funcisnp and motifbreakr, to functionally annotate risk snps for pd. the approach allows the identification of risk snp enrichment at active regulatory elements in non-coding dna (promoters […]


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FunciSNP institution(s)
Norris Cancer Center, Department of Preventive Medicine, Epigenome Center and Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA

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