SNPlocs.Hsapiens.dbSNP144.GRCh37
This is the released version of SNPlocs.Hsapiens.dbSNP144.GRCh37; for the devel version, see SNPlocs.Hsapiens.dbSNP144.GRCh37.
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3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1
SNP locations for Homo sapiens (dbSNP Build 144)
Bioconductor version: 3.23 · Package version: 0.99.20
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"):
Hervé Pagès. SNPlocs.Hsapiens.dbSNP144.GRCh37: SNP locations for Homo sapiens (dbSNP Build 144). doi:10.18129/B9.bioc.SNPlocs.Hsapiens.dbSNP144.GRCh37, R package version 0.99.20, https://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP144.GRCh37.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") 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.
Details
| Version | 0.99.20 |
| License | Artistic-2.0 |
| Last updated | 2017-01-18 |
| In Bioconductor since | BioC 3.1 (R-3.2) (11 years) |
| Downloads rank | 84 of 928 |
| Source branch | RELEASE_3_23 |
| biocViews | AnnotationData, Genetics, Homo_sapiens, SNPlocs |
| Package Short Url | https://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP144.GRCh37/ |
Documentation
| Reference Manual |
Download
Follow the installation instructions to use this package in your R session.
| Source package | SNPlocs.Hsapiens.dbSNP144.GRCh37_0.99.20.tar.gz |
| Package Downloads Report | Download Stats |
Dependencies
Depends: BSgenome (>= 1.43.4)
Imports: methods, utils, BiocGenerics, S4Vectors, IRanges, GenomeInfoDb, GenomicRanges, BSgenome
Suggests: Biostrings, BSgenome.Hsapiens.UCSC.hg19
Reverse dependencies
Imports Me (1): appreci8R
Suggests Me (13): 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