To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("FunciSNP")

In most cases, you don't need to download the package archive at all.

FunciSNP

 

Integrating Functional Non-coding Datasets with Genetic Association Studies to Identify Candidate Regulatory SNPs

Bioconductor version: Release (3.1)

FunciSNP integrates information from GWAS, 1000genomes and chromatin feature to identify functional SNP in coding or non-coding regions.

Author: Simon G. Coetzee <simon at simoncoetzee.com> and Houtan Noushmehr, PhD <houtan at usp.br>

Maintainer: Simon G. Coetzee <simon at simoncoetzee.com>

Citation (from within R, enter citation("FunciSNP")):

Installation

To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("FunciSNP")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("FunciSNP")

 

PDF R Script FunciSNP Vignette
PDF   Reference Manual
Text   NEWS

Details

biocViews Annotation, DataImport, DataRepresentation, Infrastructure, SequenceMatching, Software
Version 1.10.0
In Bioconductor since BioC 2.11 (R-2.15) (2.5 years)
License GPL-3
Depends R (>= 2.14.0), ggplot2, TxDb.Hsapiens.UCSC.hg19.knownGene, FunciSNP.data
Imports AnnotationDbi, IRanges, Rsamtools(>= 1.6.1), rtracklayer(>= 1.14.1), methods, ChIPpeakAnno(>= 2.2.0), GenomicRanges, VariantAnnotation, plyr, org.Hs.eg.db, snpStats, ggplot2 (>= 0.9.0), reshape (>= 0.8.4), scales
LinkingTo
Suggests
SystemRequirements
Enhances parallel
URL http://coetzeeseq.usc.edu/publication/Coetzee_SG_et_al_2012/
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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Package Source FunciSNP_1.10.0.tar.gz
Windows Binary FunciSNP_1.10.0.zip
Mac OS X 10.6 (Snow Leopard) FunciSNP_1.10.0.tgz
Mac OS X 10.9 (Mavericks) FunciSNP_1.10.0.tgz
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