XtraSNPlocs.Hsapiens.dbSNP144.GRCh38
This is the development version of XtraSNPlocs.Hsapiens.dbSNP144.GRCh38; for the stable release version, see XtraSNPlocs.Hsapiens.dbSNP144.GRCh38.
Extra SNP locations for Homo sapiens (dbSNP Build 144)
Bioconductor version: Development (3.24)
Extra 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 30, 2015, and contain SNPs mapped to reference genome GRCh38.p2 (a patched version of GRCh38 that doesn't alter chromosomes 1-22, X, Y, MT). While the SNPlocs.Hsapiens.dbSNP144.GRCh38 package contains only molecular variations of class "snp", this package contains molecular variations of other classes (in-del, heterozygous, microsatellite, named-locus, no-variation, mixed, and multinucleotide-polymorphism).
Author: Herve Pages
Maintainer: H. Pages <hpages at fhcrc.org>
citation("XtraSNPlocs.Hsapiens.dbSNP144.GRCh38")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("XtraSNPlocs.Hsapiens.dbSNP144.GRCh38")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| Reference Manual |
Details
| biocViews | AnnotationData, Genetics, Homo_sapiens, XtraSNPlocs |
| Version | 0.99.12 |
| License | Artistic-2.0 |
| Depends | R (>= 2.10), BSgenome |
| Imports | methods, utils, BiocGenerics, S4Vectors, IRanges, GenomeInfoDb, GenomicRanges, BSgenome |
| System Requirements | |
| URL |
See More
| Suggests | Biostrings, BSgenome.Hsapiens.UCSC.hg38, SNPlocs.Hsapiens.dbSNP144.GRCh38 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | BSgenome |
| Links To Me |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | XtraSNPlocs.Hsapiens.dbSNP144.GRCh38_0.99.12.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Package Short Url | https://bioconductor.org/packages/XtraSNPlocs.Hsapiens.dbSNP144.GRCh38/ |
| Package Downloads Report | Download Stats |