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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("SNPlocs.Hsapiens.dbSNP.20120608")
In most cases, you don't need to download the package archive at all.
SNPlocs.Hsapiens.dbSNP.20120608
SNP locations for Homo sapiens (dbSNP Build 137)
Bioconductor version: 3.0
SNP locations and alleles for Homo sapiens extracted from NCBI dbSNP Build 137. The source data files used for this package were created by NCBI on June 7-8, 2012, and contain SNPs mapped to reference genome GRCh37.p5. WARNING: Note that the GRCh37.p5 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: Herve Pages
Maintainer: H. Pages <hpages at fhcrc.org>
Citation (from within R,
enter citation("SNPlocs.Hsapiens.dbSNP.20120608")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("SNPlocs.Hsapiens.dbSNP.20120608")
Documentation
| Reference Manual |
Details
| biocViews | AnnotationData, Genetics, Homo_sapiens |
| Version | 0.99.9 |
| License | Artistic-2.0 |
| Depends | R (>= 2.10), IRanges, GenomicRanges, BSgenome(>= 1.25.6) |
| Imports | methods, utils, IRanges, GenomicRanges, BSgenome |
| LinkingTo | |
| Suggests | Biostrings, BSgenome.Hsapiens.UCSC.hg19(>= 1.3.19) |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | ggtut |
| Imports Me | |
| Suggests Me | AllelicImbalance, cheung2010, GGtools, VariantFiltering |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | SNPlocs.Hsapiens.dbSNP.20120608_0.99.9.tar.gz |
| Windows Binary | SNPlocs.Hsapiens.dbSNP.20120608_0.99.9.zip |
| Mac OS X 10.6 (Snow Leopard) | SNPlocs.Hsapiens.dbSNP.20120608_0.99.9.tgz |
| Mac OS X 10.9 (Mavericks) | SNPlocs.Hsapiens.dbSNP.20120608_0.99.9.tgz |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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