FunciSNP

This package is for version 3.9 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see FunciSNP.data.

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


Bioconductor version: 3.9

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 (version "3.6") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("FunciSNP")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

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

browseVignettes("FunciSNP")
FunciSNP Vignette PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews Annotation, DataImport, DataRepresentation, Infrastructure, SequenceMatching, Software
Version 1.28.0
In Bioconductor since BioC 2.11 (R-2.15) (11.5 years)
License GPL-3
Depends R (>= 2.14.0), ggplot2, TxDb.Hsapiens.UCSC.hg19.knownGene, FunciSNP.data
Imports methods, BiocGenerics, Biobase, S4Vectors, IRanges, GenomicRanges, Rsamtools(>= 1.6.1), rtracklayer(>= 1.14.1), ChIPpeakAnno(>= 2.2.0), VariantAnnotation, plyr, snpStats, ggplot2 (>= 0.9.0), reshape (>= 0.8.4), scales
System Requirements
URL http://coetzeeseq.usc.edu/publication/Coetzee_SG_et_al_2012/
See More
Suggests org.Hs.eg.db
Linking To
Enhances parallel
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package FunciSNP_1.28.0.tar.gz
Windows Binary FunciSNP_1.28.0.zip
Mac OS X 10.11 (El Capitan) FunciSNP_1.28.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/FunciSNP
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/FunciSNP
Bioc Package Browser https://code.bioconductor.org/browse/FunciSNP/
Package Short Url https://bioconductor.org/packages/FunciSNP/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive