To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("FunciSNP")

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

FunciSNP

This package is for version 2.12 of Bioconductor; for the stable, up-to-date release version, see FunciSNP.

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

Bioconductor version: 2.12

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")):

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("FunciSNP")

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		UCSC_genomeviewer_glioma.pdf
PDF		Reference Manual
Text		NEWS

biocViews	Annotation, DataImport, DataRepresentation, Infrastructure, SequenceMatching, Software
Version	1.2.0
In Bioconductor since	BioC 2.11 (R-2.15) (3.5 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

Follow Installation instructions to use this package in your R session.

Package Source	FunciSNP_1.2.0.tar.gz
Windows Binary	FunciSNP_1.2.0.zip
Mac OS X 10.6 (Snow Leopard)	FunciSNP_1.2.0.tgz
Subversion source	(username/password: readonly)
Git source	https://github.com/Bioconductor-mirror/FunciSNP/tree/release-2.12
Package Short Url	http://bioconductor.org/packages/FunciSNP/
Package Downloads Report	Download Stats

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