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>
Citation (from within R,
enter citation("BSgenome")
):
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
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R Script
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Efficient genome searching with Biostrings and the BSgenome data packages |
PDF
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R Script
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How to forge a BSgenome data package |
PDF
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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 |
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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 |
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Enhances |
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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 |
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Build Report |
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Package Archives
Follow
Installation instructions to use this
package in your R session.