FunciSNP

DOI: 10.18129/B9.bioc.FunciSNP    

This package is for version 3.10 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: 3.10

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 (!requireNamespace("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")

 

PDF R Script FunciSNP Vignette
PDF   Reference Manual
Text   NEWS

Details

biocViews Annotation, DataImport, DataRepresentation, Infrastructure, SequenceMatching, Software
Version 1.30.0
In Bioconductor since BioC 2.11 (R-2.15) (7.5 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
LinkingTo
Suggests org.Hs.eg.db
SystemRequirements
Enhances parallel
URL http://coetzeeseq.usc.edu/publication/Coetzee_SG_et_al_2012/
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package FunciSNP_1.30.0.tar.gz
Windows Binary FunciSNP_1.30.0.zip
Mac OS X 10.11 (El Capitan) FunciSNP_1.30.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/FunciSNP
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/FunciSNP
Package Short Url https://bioconductor.org/packages/FunciSNP/
Package Downloads Report Download Stats

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