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("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 | R Script | |
| Reference Manual | ||
| 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 |