FunciSNP pipeline

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 1.10.0
Stability Stable
Requirements ggplot, TxDb.Hsapiens.UCSC.hg19.knownGene, FunciSNP.data
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)
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 funcisnp21, 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 […]

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

[…] 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 from gencode v15. we ran funcisnp with the following parameters: ±200 kb around each of the 25 tag snps and r2>0.1. to analyze the potential effects of correlated snps on protein coding, we employed snpeff and provean […]

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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