FunciSNP

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

Bioconductor version: Development (3.0)

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>

To install this package, start R and enter:

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

To cite this package in a publication, start R and enter:

    citation("FunciSNP")

Documentation

PDF R Script FunciSNP Vignette
PDF   Reference Manual
Text   NEWS

Details

biocViews Annotation, DataImport, DataRepresentation, Infrastructure, SequenceMatching, Software
Version 1.7.0
In Bioconductor since BioC 2.11 (R-2.15)
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
Suggests
System Requirements
URL http://coetzeeseq.usc.edu/publication/Coetzee_SG_et_al_2012/
Depends On Me
Imports Me
Suggests Me

Package Downloads

Package Source FunciSNP_1.7.0.tar.gz
Windows Binary FunciSNP_1.7.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) FunciSNP_1.7.0.tgz
Mac OS X 10.9 (Mavericks)
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