SNPlocs.Hsapiens.dbSNP144.GRCh37

DOI: 10.18129/B9.bioc.SNPlocs.Hsapiens.dbSNP144.GRCh37    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see SNPlocs.Hsapiens.dbSNP144.GRCh37.

SNP locations for Homo sapiens (dbSNP Build 144)

Bioconductor version: 3.9

SNP locations and alleles for Homo sapiens extracted from NCBI dbSNP Build 144. The source data files used for this package were created by NCBI on May 29-30, 2015, and contain SNPs mapped to reference genome GRCh37.p13. WARNING: Note that the GRCh37.p13 genome is a patched version of GRCh37. However 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 position but this injection will exclude chrM (i.e. nothing will be injected in that sequence).

Author: Hervé Pagès

Maintainer: H. Pagès <hpages at fredhutch.org>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("SNPlocs.Hsapiens.dbSNP144.GRCh37")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

PDF		Reference Manual

Details

biocViews	AnnotationData, Genetics, Homo_sapiens, SNPlocs
Version	0.99.20
License	Artistic-2.0
Depends	BSgenome(>= 1.43.4)
Imports	methods, utils, BiocGenerics, S4Vectors, IRanges, GenomeInfoDb, GenomicRanges, BSgenome
LinkingTo
Suggests	Biostrings, BSgenome.Hsapiens.UCSC.hg19
SystemRequirements
Enhances
URL
Depends On Me	eQTL
Imports Me	appreci8R
Suggests Me	AllelicImbalance, GenomicScores, GGtools, MafDb.1Kgenomes.phase1.hs37d5, MafDb.1Kgenomes.phase3.hs37d5, MafDb.ESP6500SI.V2.SSA137.hs37d5, MafDb.ExAC.r1.0.hs37d5, MafDb.ExAC.r1.0.nonTCGA.hs37d5, MafDb.gnomAD.r2.1.hs37d5, MafDb.gnomADex.r2.1.hs37d5, MafDb.TOPMed.freeze5.hg19, VariantFiltering, XtraSNPlocs.Hsapiens.dbSNP144.GRCh37
Links To Me

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	SNPlocs.Hsapiens.dbSNP144.GRCh37_0.99.20.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan)
Package Short Url	https://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP144.GRCh37/
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