BSgenome
This package is for version 3.2 of Bioconductor;
for the stable, up-to-date release version, see
BSgenome.
Infrastructure for Biostrings-based genome data packages and support for efficient SNP representation
Bioconductor version: 3.2
Infrastructure shared by all the Biostrings-based genome data packages
Author: Herve Pages
Maintainer: H. Pages <hpages at fredhutch.org>
Citation (from within R,
enter citation("BSgenome")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("BSgenome")
Documentation
To view documentation for the version of this package installed
in your system, start R and enter:
browseVignettes("BSgenome")
PDF
Efficient genome searching with Biostrings and the BSgenome data packages
PDF
How to forge a BSgenome data package
Details
Version
1.38.0
In Bioconductor since
BioC 1.9 (R-2.4) (9.5 years)
License
Artistic-2.0
Imports
methods, stats,
BiocGenerics,
S4Vectors,
IRanges,
XVector,
GenomeInfoDb,
GenomicRanges,
Biostrings,
Rsamtools,
rtracklayer
LinkingTo
Suggests
BiocInstaller,
Biobase,
BSgenome.Celegans.UCSC.ce2,
BSgenome.Hsapiens.UCSC.hg38,
BSgenome.Hsapiens.UCSC.hg38.masked,
BSgenome.Mmusculus.UCSC.mm10,
BSgenome.Rnorvegicus.UCSC.rn5,
TxDb.Hsapiens.UCSC.hg38.knownGene,
TxDb.Mmusculus.UCSC.mm10.knownGene,
SNPlocs.Hsapiens.dbSNP141.GRCh38,
XtraSNPlocs.Hsapiens.dbSNP141.GRCh38,
hgu95av2probe,
RUnit
SystemRequirements
Enhances
Depends On Me
BSgenome.Alyrata.JGI.v1,
BSgenome.Amellifera.BeeBase.assembly4,
BSgenome.Amellifera.UCSC.apiMel2,
BSgenome.Amellifera.UCSC.apiMel2.masked,
BSgenome.Athaliana.TAIR.04232008,
BSgenome.Athaliana.TAIR.TAIR9,
BSgenome.Btaurus.UCSC.bosTau3,
BSgenome.Btaurus.UCSC.bosTau3.masked,
BSgenome.Btaurus.UCSC.bosTau4,
BSgenome.Btaurus.UCSC.bosTau4.masked,
BSgenome.Btaurus.UCSC.bosTau6,
BSgenome.Btaurus.UCSC.bosTau6.masked,
BSgenome.Btaurus.UCSC.bosTau8,
BSgenome.Celegans.UCSC.ce10,
BSgenome.Celegans.UCSC.ce11,
BSgenome.Celegans.UCSC.ce2,
BSgenome.Celegans.UCSC.ce6,
BSgenome.Cfamiliaris.UCSC.canFam2,
BSgenome.Cfamiliaris.UCSC.canFam2.masked,
BSgenome.Cfamiliaris.UCSC.canFam3,
BSgenome.Cfamiliaris.UCSC.canFam3.masked,
BSgenome.Dmelanogaster.UCSC.dm2,
BSgenome.Dmelanogaster.UCSC.dm2.masked,
BSgenome.Dmelanogaster.UCSC.dm3,
BSgenome.Dmelanogaster.UCSC.dm3.masked,
BSgenome.Dmelanogaster.UCSC.dm6,
BSgenome.Drerio.UCSC.danRer10,
BSgenome.Drerio.UCSC.danRer5,
BSgenome.Drerio.UCSC.danRer5.masked,
BSgenome.Drerio.UCSC.danRer6,
BSgenome.Drerio.UCSC.danRer6.masked,
BSgenome.Drerio.UCSC.danRer7,
BSgenome.Drerio.UCSC.danRer7.masked,
BSgenome.Ecoli.NCBI.20080805,
BSgenome.Gaculeatus.UCSC.gasAcu1,
BSgenome.Gaculeatus.UCSC.gasAcu1.masked,
BSgenome.Ggallus.UCSC.galGal3,
BSgenome.Ggallus.UCSC.galGal3.masked,
BSgenome.Ggallus.UCSC.galGal4,
BSgenome.Ggallus.UCSC.galGal4.masked,
BSgenome.Hsapiens.1000genomes.hs37d5,
BSgenome.Hsapiens.NCBI.GRCh38,
BSgenome.Hsapiens.UCSC.hg17,
BSgenome.Hsapiens.UCSC.hg17.masked,
BSgenome.Hsapiens.UCSC.hg18,
BSgenome.Hsapiens.UCSC.hg18.masked,
BSgenome.Hsapiens.UCSC.hg19,
BSgenome.Hsapiens.UCSC.hg19.masked,
BSgenome.Hsapiens.UCSC.hg38,
BSgenome.Hsapiens.UCSC.hg38.masked,
BSgenome.Mfascicularis.NCBI.5.0,
BSgenome.Mfuro.UCSC.musFur1,
BSgenome.Mmulatta.UCSC.rheMac2,
BSgenome.Mmulatta.UCSC.rheMac2.masked,
BSgenome.Mmulatta.UCSC.rheMac3,
BSgenome.Mmulatta.UCSC.rheMac3.masked,
BSgenome.Mmusculus.UCSC.mm10,
BSgenome.Mmusculus.UCSC.mm10.masked,
BSgenome.Mmusculus.UCSC.mm8,
BSgenome.Mmusculus.UCSC.mm8.masked,
BSgenome.Mmusculus.UCSC.mm9,
BSgenome.Mmusculus.UCSC.mm9.masked,
BSgenome.Osativa.MSU.MSU7,
BSgenome.Ptroglodytes.UCSC.panTro2,
BSgenome.Ptroglodytes.UCSC.panTro2.masked,
BSgenome.Ptroglodytes.UCSC.panTro3,
BSgenome.Ptroglodytes.UCSC.panTro3.masked,
BSgenome.Rnorvegicus.UCSC.rn4,
BSgenome.Rnorvegicus.UCSC.rn4.masked,
BSgenome.Rnorvegicus.UCSC.rn5,
BSgenome.Rnorvegicus.UCSC.rn5.masked,
BSgenome.Rnorvegicus.UCSC.rn6,
BSgenome.Scerevisiae.UCSC.sacCer1,
BSgenome.Scerevisiae.UCSC.sacCer2,
BSgenome.Scerevisiae.UCSC.sacCer3,
BSgenome.Sscrofa.UCSC.susScr3,
BSgenome.Sscrofa.UCSC.susScr3.masked,
BSgenome.Tgondii.ToxoDB.7.0,
BSgenome.Tguttata.UCSC.taeGut1,
BSgenome.Tguttata.UCSC.taeGut1.masked,
BSgenome.Tguttata.UCSC.taeGut2,
BSgenome.Vvinifera.URGI.IGGP12Xv0,
BSgenome.Vvinifera.URGI.IGGP12Xv2,
CAGEr,
cleanUpdTSeq,
GOTHiC,
htSeqTools,
leeBamViews,
MEDIPS,
motifRG,
REDseq,
regioneR,
rGADEM,
SNPlocs.Hsapiens.dbSNP.20090506,
SNPlocs.Hsapiens.dbSNP.20120608,
SNPlocs.Hsapiens.dbSNP141.GRCh38,
SNPlocs.Hsapiens.dbSNP142.GRCh37,
SNPlocs.Hsapiens.dbSNP144.GRCh37,
SNPlocs.Hsapiens.dbSNP144.GRCh38,
XtraSNPlocs.Hsapiens.dbSNP141.GRCh38,
XtraSNPlocs.Hsapiens.dbSNP144.GRCh37,
XtraSNPlocs.Hsapiens.dbSNP144.GRCh38
Imports Me
BEAT,
BSgenome.Alyrata.JGI.v1,
BSgenome.Amellifera.BeeBase.assembly4,
BSgenome.Amellifera.UCSC.apiMel2,
BSgenome.Amellifera.UCSC.apiMel2.masked,
BSgenome.Athaliana.TAIR.04232008,
BSgenome.Athaliana.TAIR.TAIR9,
BSgenome.Btaurus.UCSC.bosTau3,
BSgenome.Btaurus.UCSC.bosTau3.masked,
BSgenome.Btaurus.UCSC.bosTau4,
BSgenome.Btaurus.UCSC.bosTau4.masked,
BSgenome.Btaurus.UCSC.bosTau6,
BSgenome.Btaurus.UCSC.bosTau6.masked,
BSgenome.Btaurus.UCSC.bosTau8,
BSgenome.Celegans.UCSC.ce10,
BSgenome.Celegans.UCSC.ce11,
BSgenome.Celegans.UCSC.ce2,
BSgenome.Celegans.UCSC.ce6,
BSgenome.Cfamiliaris.UCSC.canFam2,
BSgenome.Cfamiliaris.UCSC.canFam2.masked,
BSgenome.Cfamiliaris.UCSC.canFam3,
BSgenome.Cfamiliaris.UCSC.canFam3.masked,
BSgenome.Dmelanogaster.UCSC.dm2,
BSgenome.Dmelanogaster.UCSC.dm2.masked,
BSgenome.Dmelanogaster.UCSC.dm3,
BSgenome.Dmelanogaster.UCSC.dm3.masked,
BSgenome.Dmelanogaster.UCSC.dm6,
BSgenome.Drerio.UCSC.danRer10,
BSgenome.Drerio.UCSC.danRer5,
BSgenome.Drerio.UCSC.danRer5.masked,
BSgenome.Drerio.UCSC.danRer6,
BSgenome.Drerio.UCSC.danRer6.masked,
BSgenome.Drerio.UCSC.danRer7,
BSgenome.Drerio.UCSC.danRer7.masked,
BSgenome.Ecoli.NCBI.20080805,
BSgenome.Gaculeatus.UCSC.gasAcu1,
BSgenome.Gaculeatus.UCSC.gasAcu1.masked,
BSgenome.Ggallus.UCSC.galGal3,
BSgenome.Ggallus.UCSC.galGal3.masked,
BSgenome.Ggallus.UCSC.galGal4,
BSgenome.Ggallus.UCSC.galGal4.masked,
BSgenome.Hsapiens.NCBI.GRCh38,
BSgenome.Hsapiens.UCSC.hg17,
BSgenome.Hsapiens.UCSC.hg17.masked,
BSgenome.Hsapiens.UCSC.hg18,
BSgenome.Hsapiens.UCSC.hg18.masked,
BSgenome.Hsapiens.UCSC.hg19,
BSgenome.Hsapiens.UCSC.hg19.masked,
BSgenome.Hsapiens.UCSC.hg38,
BSgenome.Hsapiens.UCSC.hg38.masked,
BSgenome.Mfascicularis.NCBI.5.0,
BSgenome.Mfuro.UCSC.musFur1,
BSgenome.Mmulatta.UCSC.rheMac2,
BSgenome.Mmulatta.UCSC.rheMac2.masked,
BSgenome.Mmulatta.UCSC.rheMac3,
BSgenome.Mmulatta.UCSC.rheMac3.masked,
BSgenome.Mmusculus.UCSC.mm10,
BSgenome.Mmusculus.UCSC.mm10.masked,
BSgenome.Mmusculus.UCSC.mm8,
BSgenome.Mmusculus.UCSC.mm8.masked,
BSgenome.Mmusculus.UCSC.mm9,
BSgenome.Mmusculus.UCSC.mm9.masked,
BSgenome.Osativa.MSU.MSU7,
BSgenome.Ptroglodytes.UCSC.panTro2,
BSgenome.Ptroglodytes.UCSC.panTro2.masked,
BSgenome.Ptroglodytes.UCSC.panTro3,
BSgenome.Ptroglodytes.UCSC.panTro3.masked,
BSgenome.Rnorvegicus.UCSC.rn4,
BSgenome.Rnorvegicus.UCSC.rn4.masked,
BSgenome.Rnorvegicus.UCSC.rn5,
BSgenome.Rnorvegicus.UCSC.rn5.masked,
BSgenome.Rnorvegicus.UCSC.rn6,
BSgenome.Scerevisiae.UCSC.sacCer1,
BSgenome.Scerevisiae.UCSC.sacCer2,
BSgenome.Scerevisiae.UCSC.sacCer3,
BSgenome.Sscrofa.UCSC.susScr3,
BSgenome.Sscrofa.UCSC.susScr3.masked,
BSgenome.Tgondii.ToxoDB.7.0,
BSgenome.Tguttata.UCSC.taeGut1,
BSgenome.Tguttata.UCSC.taeGut1.masked,
BSgenome.Tguttata.UCSC.taeGut2,
BSgenome.Vvinifera.URGI.IGGP12Xv0,
BSgenome.Vvinifera.URGI.IGGP12Xv2,
charm,
ChIPpeakAnno,
cobindR,
CRISPRseek,
diffHic,
genomation,
ggbio,
gmapR,
GreyListChIP,
GUIDEseq,
Gviz,
hiAnnotator,
InPAS,
MethylSeekR,
motifbreakR,
phastCons100way.UCSC.hg19,
phastCons100way.UCSC.hg38,
phastCons7way.UCSC.hg38,
PING,
podkat,
QuasR,
R453Plus1Toolbox,
regioneR,
Repitools,
seqplots,
SNPlocs.Hsapiens.dbSNP.20090506,
SNPlocs.Hsapiens.dbSNP.20120608,
SNPlocs.Hsapiens.dbSNP141.GRCh38,
SNPlocs.Hsapiens.dbSNP142.GRCh37,
SNPlocs.Hsapiens.dbSNP144.GRCh37,
SNPlocs.Hsapiens.dbSNP144.GRCh38,
TFBSTools,
VariantAnnotation,
VariantFiltering,
VariantTools,
XtraSNPlocs.Hsapiens.dbSNP141.GRCh38,
XtraSNPlocs.Hsapiens.dbSNP144.GRCh37,
XtraSNPlocs.Hsapiens.dbSNP144.GRCh38
Suggests Me
Biostrings,
biovizBase,
chipseq,
easyRNASeq,
GeneRegionScan,
GenomeInfoDb,
GenomicAlignments,
GenomicFeatures,
GenomicRanges,
genoset,
metaseqR,
MiRaGE,
oneChannelGUI,
QDNAseq,
rtracklayer,
SNPlocs.Hsapiens.dbSNP.20100427,
SNPlocs.Hsapiens.dbSNP.20101109,
SNPlocs.Hsapiens.dbSNP.20110815,
SNPlocs.Hsapiens.dbSNP.20111119,
spliceR,
waveTiling
Package Archives
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