FunciSNP

DOI: 10.18129/B9.bioc.FunciSNP    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.12 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: 3.12

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>

Installation

To install this package, start R (version "4.0") 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	1.34.0
In Bioconductor since	BioC 2.11 (R-2.15) (8.5 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_1.34.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra)
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