BSgenome.Hsapiens.UCSC.hg38

This is the released version of BSgenome.Hsapiens.UCSC.hg38; for the devel version, see BSgenome.Hsapiens.UCSC.hg38.

Full genomic sequences for Homo sapiens (UCSC genome hg38)

Bioconductor version: Release (3.23)

Full genomic sequences for Homo sapiens as provided by UCSC (genome hg38, based on assembly GRCh38.p14 since 2023/01/31). The sequences are stored in DNAString objects.

Author: The Bioconductor Dev Team

Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>

Citation (from within R, enter citation("BSgenome.Hsapiens.UCSC.hg38")):

Seminal Bioconductor project articles:

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")

BiocManager::install("BSgenome.Hsapiens.UCSC.hg38")

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

Documentation


Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	AnnotationData, BSgenome, Genetics, Homo_sapiens
Version	1.4.5
License	Artistic-2.0
Depends	R (>= 4.2.0), GenomeInfoDb(>= 1.34.9), BSgenome(>= 1.66.2)
Imports
System Requirements
URL

Suggests
Linking To
Enhances
Depends On Me	BSgenome.Hsapiens.UCSC.hg38.masked
Imports Me	branchpointer, cfDNAPro, epiregulon, katdetectr, musicatk, ORFhunteR, primirTSS, TENET, OHCA
Suggests Me	BSgenome, bsseq, BUSpaRse, ChIPpeakAnno, circRNAprofiler, CleanUpRNAseq, CNEr, crisprBowtie, crisprBwa, crisprDesign, CRISPRseek, crisprShiny, crisprViz, DegCre, DMRcaller, DOTSeq, eisaR, enhancerHomologSearch, EpiCompare, epiSeeker, EpiTxDb, FRASER, GenomicRanges, GenomicScores, GenVisR, GRaNIE, GUIDEseq, HiCDCPlus, MethReg, MethylSeekR, MIRit, Motif2Site, MotifPeeker, multicrispr, MutSeqR, nullranges, periodicDNA, pqsfinder, RAIDS, REMP, scanMiRApp, SCOPE, SEMPLR, Seqinfo, signeR, supersigs, TAPseq, transmogR, BSgenome.Hsapiens.UCSC.hg38.dbSNP151.major, BSgenome.Hsapiens.UCSC.hg38.dbSNP151.minor, SNPlocs.Hsapiens.dbSNP144.GRCh38, SNPlocs.Hsapiens.dbSNP149.GRCh38, SNPlocs.Hsapiens.dbSNP150.GRCh38, SNPlocs.Hsapiens.dbSNP155.GRCh38, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38, ActiveDriverWGS, GencoDymo2, gwas2crispr, revert, SATS, TmCalculator
Links To Me

Package Archives

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

Source Package	BSgenome.Hsapiens.UCSC.hg38_1.4.5.tar.gz
Windows Binary (x86_64)
macOS Binary (big-sur-x86_64)
macOS Binary (sonoma-arm64)
Package Short Url	https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg38/
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