BSgenome

DOI: 10.18129/B9.bioc.BSgenome    

This is the development version of BSgenome; for the stable release version, see BSgenome.

Software infrastructure for efficient representation of full genomes and their SNPs

Bioconductor version: Development (3.17)

Infrastructure shared by all the Biostrings-based genome data packages.

Author: Hervé Pagès

Maintainer: H. Pagès <hpages.on.github at gmail.com>

Installation

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

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("BSgenome")

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("BSgenome")

 

PDF	R Script	Efficient genome searching with Biostrings and the BSgenome data packages
PDF	R Script	How to forge a BSgenome data package
PDF		Reference Manual

Details

biocViews	Annotation, DataRepresentation, Genetics, Infrastructure, SNP, SequenceMatching, Software
Version	1.67.0
In Bioconductor since	BioC 1.9 (R-2.4) (16 years)
License	Artistic-2.0
Depends	R (>= 2.8.0), methods, BiocGenerics(>= 0.13.8), S4Vectors(>= 0.17.28), IRanges(>= 2.13.16), GenomeInfoDb(>= 1.25.6), GenomicRanges(>= 1.31.10), Biostrings(>= 2.47.6), rtracklayer(>= 1.39.7)
Imports	methods, utils, stats, matrixStats, BiocGenerics, S4Vectors, IRanges, XVector(>= 0.29.3), GenomeInfoDb, GenomicRanges, Biostrings, Rsamtools, rtracklayer
LinkingTo
Suggests	BiocManager, Biobase, BSgenome.Celegans.UCSC.ce2, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38.masked, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Rnorvegicus.UCSC.rn5, BSgenome.Scerevisiae.UCSC.sacCer1, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh38, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38, hgu95av2probe, RUnit
SystemRequirements
Enhances
URL	https://bioconductor.org/packages/BSgenome
BugReports	https://github.com/Bioconductor/BSgenome/issues
Depends On Me	annotation, bambu, ChIPanalyser, GOTHiC, HelloRanges, leeBamViews, MEDIPS, periodicDNA, REDseq, rGADEM, VarCon
Imports Me	AllelicImbalance, appreci8R, ATACseqQC, atSNP, BEAT, bsseq, BUSpaRse, CAGEr, chromVAR, circRNAprofiler, cleanUpdTSeq, cliProfiler, crisprBowtie, crisprBwa, crisprDesign, CRISPRseek, crisprseekplus, crisprViz, diffHic, dpeak, enhancerHomologSearch, enrichTF, esATAC, EventPointer, exomePeak2, FRASER, gcapc, genomation, GenomicDistributionsData, GenVisR, ggbio, gmapR, GreyListChIP, GUIDEseq, Gviz, hiAnnotator, HiCDCPlus, InPAS, IsoformSwitchAnalyzeR, katdetectr, m6Aboost, MADSEQ, methrix, MethylSeekR, MMDiff2, monaLisa, Motif2Site, motifbreakR, motifmatchr, msgbsR, multicrispr, MungeSumstats, musicatk, MutationalPatterns, NxtIRFcore, ORFik, PING, pipeFrame, podkat, qsea, QuasR, R453Plus1Toolbox, RareVariantVis, RCAS, regioneR, REMP, Repitools, RESOLVE, ribosomeProfilingQC, RNAmodR, scmeth, SCOPE, signeR, SigsPack, SingleMoleculeFootprinting, SparseSignatures, spatzie, spiky, SpliceWiz, TAPseq, TFBSTools, trena, tRNAscanImport, Ularcirc, UMI4Cats, VariantAnnotation, VariantFiltering, VariantTools, XNAString
Suggests Me	Biostrings, biovizBase, ChIPpeakAnno, chipseq, easyRNASeq, eisaR, factR, GeneRegionScan, GenomeInfoDb, GenomicAlignments, GenomicFeatures, GenomicRanges, maftools, metaseqR2, MiRaGE, plotgardener, ProteoDisco, PWMEnrich, QDNAseq, recoup, RiboCrypt, rtracklayer, sitadela
Links To Me
Build Report

Package Archives

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

Source Package	BSgenome_1.67.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/BSgenome
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/BSgenome
Package Short Url	https://bioconductor.org/packages/BSgenome/
Package Downloads Report	Download Stats