FunciSNP protocols

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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


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Documentation


Maintainer


  • person_outline Simon G. Coetzee <>

Publication for FunciSNP

FunciSNP in pipelines

 (2)
2015
PMCID: 4572072
PMID: 26025378
DOI: 10.1093/hmg/ddv203

[…] prca encode datasets of chromatin features to identify putative regulatory regions at each risk locus (,). the integration of chromatin bio-feature annotations with snp positions was performed using funcisnp (). these datasets included lncap and rwpei dnase i hs sites (gse32970) encode; prec dnase i hs sites (gse29692) encode; lncap ctcf chip-seq peaks (gse33213) encode; lncap h3k27ac and tcf7l2 […]

2014
PMCID: 4200523
PMID: 25268989
DOI: 10.1038/ncomms6114

[…] (illumina), comparing the deleted cells to parental hct116 cells., to identify snps correlated with the 25 crc tag snps and those that overlap with chromatin biofeatures, we use the r package for funcisnp, which is available in bioconductor. we used h3k27ac chip-seq data from hct116 cells and sigmoid colon tissue and as biofeatures we used exon, intron, utr and tss annotations generated […]


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FunciSNP in publications

 (17)
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 […]

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, […]

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 […]

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) […]

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 […]


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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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