- Home
- Bioconductor 3.2
- Annotation Packages
- SNPlocs.Hsapiens.dbSNP142.GRCh37
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("SNPlocs.Hsapiens.dbSNP142.GRCh37")
In most cases, you don't need to download the package archive at all.
SNPlocs.Hsapiens.dbSNP142.GRCh37
|
SNP locations for Homo sapiens (dbSNP Build 142)
Bioconductor version: 3.2
SNP locations and alleles for Homo sapiens extracted from NCBI dbSNP Build 142. The source data files used for this package were created by NCBI on October 14, 2014, and contain SNPs mapped to reference genome GRCh37.p13. WARNING: Note that the GRCh37.p13 genome is a patched version of GRCh37 but the patch doesn't alter chromosomes 1-22, X, Y, MT. GRCh37 itself is the same as the hg19 genome from UCSC *except* for the mitochondrion chromosome. Therefore, the SNPs in this package can be "injected" in BSgenome.Hsapiens.UCSC.hg19 and they will land at the correct location but this injection will exclude chrM (i.e. nothing will be injected in that sequence).
Author: Herv\'e Pag\`es
Maintainer: Simon Coetzee <simon.coetzee at cshs.org>
Citation (from within R,
enter citation("SNPlocs.Hsapiens.dbSNP142.GRCh37")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("SNPlocs.Hsapiens.dbSNP142.GRCh37")
Documentation
| Reference Manual |
Details
| biocViews | AnnotationData, Genetics, Homo_sapiens |
| Version | 0.99.5 |
| License | Artistic-2.0 |
| Depends | R (>= 2.10), IRanges, GenomeInfoDb, GenomicRanges, BSgenome(>= 1.25.6) |
| Imports | methods, utils, IRanges, GenomeInfoDb, GenomicRanges, BSgenome |
| LinkingTo | |
| Suggests | Biostrings, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg19.masked(>= 1.3.19) |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | motifbreakR |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | SNPlocs.Hsapiens.dbSNP142.GRCh37_0.99.5.tar.gz |
| Windows Binary | |
| Mac OS X 10.6 (Snow Leopard) | |
| Mac OS X 10.9 (Mavericks) | |
| Package Short Url | http://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP142.GRCh37/ |
| Package Downloads Report | Download Stats |
Documentation »
Bioconductor
- Package vignettes and manuals.
- Workflows for learning and use.
- Course and conference material.
- Videos.
- Community resources and tutorials.
R / CRAN packages and documentation
Support »
Please read the posting guide. Post questions about Bioconductor to one of the following locations:
- Support site - for questions about Bioconductor packages
- Bioc-devel mailing list - for package developers
