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SNPlocs.Hsapiens.dbSNP144.GRCh37

SNP locations for Homo sapiens (dbSNP Build 144)

Bioconductor version: Release (3.17)

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>

Citation (from within R, enter citation("SNPlocs.Hsapiens.dbSNP144.GRCh37")):

Installation

To install this package, start R (version "4.3") and enter: 

if (!require("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

Reference Manual PDF

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
Linking To
Suggests Biostrings, BSgenome.Hsapiens.UCSC.hg19
System Requirements
Enhances
URL
See More
Depends On Me
Imports Me appreci8R
Suggests Me AllelicImbalance, GenomicScores, MafDb.1Kgenomes.phase1.hs37d5, MafDb.1Kgenomes.phase3.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, MungeSumstats, VariantAnnotation, 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
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macOS Binary (x86_64)
macOS Binary (arm64)
Package Short Url https://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP144.GRCh37/
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