To install this package, start R and enter:
## try http:// if https:// URLs are not supported source("https://bioconductor.org/biocLite.R") biocLite("VariantAnnotation")
In most cases, you don't need to download the package archive at all.
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This package is for version 2.11 of Bioconductor; for the stable, up-to-date release version, see VariantAnnotation.
Bioconductor version: 2.11
Annotate variants with respect to location and amino acid coding
Author: Valerie Obenchain, Martin Morgan, Michael Lawrence
Maintainer: Valerie Obenchain <vobencha at fhcrc.org>
Citation (from within R,
enter citation("VariantAnnotation")
):
To install this package, start R and enter:
## try http:// if https:// URLs are not supported source("https://bioconductor.org/biocLite.R") biocLite("VariantAnnotation")
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("VariantAnnotation")
R Script | Introduction to VariantAnnotation | |
Reference Manual | ||
Text | NEWS |
biocViews | Annotation, DataImport, Genetics, HighThroughputSequencing, Homo_sapiens, SNP, Sequencing, Software |
Version | 1.4.12 |
In Bioconductor since | BioC 2.9 (R-2.14) (4.5 years) |
License | Artistic-2.0 |
Depends | R (>= 2.8.0), methods, GenomicRanges(>= 1.9.56), Rsamtools(>= 1.9.4), IRanges(>= 1.15.48) |
Imports | methods, BiocGenerics(>= 0.1.0), IRanges, Biobase(>= 2.15.1), Rsamtools(>= 1.9.4), AnnotationDbi(>= 1.17.11), Biostrings(>= 2.25.2), zlibbioc, BSgenome, GenomicFeatures(>= 1.9.35), DBI |
LinkingTo | IRanges, Biostrings, Rsamtools |
Suggests | RUnit, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP.20110815, SIFT.Hsapiens.dbSNP132, PolyPhen.Hsapiens.dbSNP131, snpStats |
SystemRequirements | |
Enhances | |
URL | |
Depends On Me | cgdv17, PolyPhen.Hsapiens.dbSNP131, SIFT.Hsapiens.dbSNP132, VariantTools |
Imports Me | FunciSNP, ggbio, GGtools, gmapR, R453Plus1Toolbox, VariantTools |
Suggests Me | GenomicRanges, gmapR, GWASTools |
Build Report |
Follow Installation instructions to use this package in your R session.
Package Source | VariantAnnotation_1.4.12.tar.gz |
Windows Binary | VariantAnnotation_1.4.12.zip (32- & 64-bit) |
Mac OS X 10.6 (Snow Leopard) | |
Subversion source | (username/password: readonly) |
Git source | https://github.com/Bioconductor-mirror/VariantAnnotation/tree/release-2.11 |
Package Short Url | http://bioconductor.org/packages/VariantAnnotation/ |
Package Downloads Report | Download Stats |
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