SNPlocs.Hsapiens.dbSNP155.GRCh38
This is the development version of SNPlocs.Hsapiens.dbSNP155.GRCh38; for the stable release version, see SNPlocs.Hsapiens.dbSNP155.GRCh38.
Human SNP locations and alleles extracted from dbSNP Build 155 and placed on the GRCh38/hg38 assembly
Bioconductor version: Development (3.24)
The 949,021,448 SNPs in this package were extracted from the RefSNP JSON files for chromosomes 1-22, X, Y, and MT, located at https://ftp.ncbi.nih.gov/snp/archive/b155/JSON/ (these files were created by NCBI in May 2021). These SNPs can be "injected" in BSgenome.Hsapiens.NCBI.GRCh38 or BSgenome.Hsapiens.UCSC.hg38.
Author: Hervé Pagès
Maintainer: Hervé Pagès <hpages.on.github at gmail.com>
citation("SNPlocs.Hsapiens.dbSNP155.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("SNPlocs.Hsapiens.dbSNP155.GRCh38")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| Reference Manual |
Details
| biocViews | AnnotationData, Genetics, Homo_sapiens, SNPlocs |
| Version | 0.99.24 |
| License | Artistic-2.0 |
| Depends | R (>= 4.2.0), BSgenome(>= 1.67.2) |
| Imports | methods, utils, BiocGenerics, S4Vectors, IRanges, GenomeInfoDb, GenomicRanges, BSgenome |
| System Requirements | |
| URL |
See More
| Suggests | Biostrings, BSgenome.Hsapiens.UCSC.hg38 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | MungeSumstats |
| Links To Me |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | SNPlocs.Hsapiens.dbSNP155.GRCh38_0.99.24.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Package Short Url | https://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP155.GRCh38/ |
| Package Downloads Report | Download Stats |