$,BSgenome-method	BSgenome-class
alphabetFrequency,BSgenomeViews-method	BSgenomeViews-class
as.character,BSgenomeViews-method	BSgenomeViews-class
as.data.frame,BSgenomeViews-method	BSgenomeViews-class
as.list,BSgenome-method	BSgenome-class
available.genomes	available.genomes
available.SNPs	injectSNPs
bsapply	bsapply
BSgenome	BSgenome-class
BSgenome-class	BSgenome-class
BSgenome-utils	BSgenome-utils
BSgenomeDataPkgSeed	BSgenomeForge
BSgenomeDataPkgSeed-class	BSgenomeForge
BSgenomeForge	BSgenomeForge
BSgenomeViews	BSgenomeViews-class
BSgenomeViews-class	BSgenomeViews-class
BSParams	BSParams-class
BSParams-class	BSParams-class
class:BSgenome	BSgenome-class
class:BSgenomeDataPkgSeed	BSgenomeForge
class:BSgenomeViews	BSgenomeViews-class
class:BSParams	BSParams-class
class:InjectSNPsHandler	injectSNPs
class:SNPlocs	SNPlocs-class
class:XtraSNPlocs	XtraSNPlocs-class
coerce,BSgenomeViews,DNAStringSet-method	BSgenomeViews-class
coerce,BSgenomeViews,XStringSet-method	BSgenomeViews-class
colnames,XtraSNPlocs-method	XtraSNPlocs-class
commonName,SNPlocs-method	SNPlocs-class
commonName,XtraSNPlocs-method	XtraSNPlocs-class
compatibleGenomes	SNPlocs-class
compatibleGenomes,SNPlocs-method	SNPlocs-class
consensusMatrix,BSgenomeViews-method	BSgenomeViews-class
consensusString,BSgenomeViews-method	BSgenomeViews-class
countPWM,BSgenome-method	BSgenome-utils
dim,XtraSNPlocs-method	XtraSNPlocs-class
elementNROWS,BSgenomeViews-method	BSgenomeViews-class
end,BSgenomeViews-method	BSgenomeViews-class
export,BSgenome,FastaFile,ANY-method	export-methods
export,BSgenome,TwoBitFile,ANY-method	export-methods
export-methods	export-methods
extractROWS,BSgenomeViews-method	BSgenomeViews-class
forgeBSgenomeDataPkg	BSgenomeForge
forgeBSgenomeDataPkg,BSgenomeDataPkgSeed-method	BSgenomeForge
forgeBSgenomeDataPkg,character-method	BSgenomeForge
forgeBSgenomeDataPkg,list-method	BSgenomeForge
forgeMasksFiles	BSgenomeForge
forgeSeqFiles	BSgenomeForge
forgeSeqlengthsFile	BSgenomeForge
getBSgenome	available.genomes
getListElement,BSgenomeViews-method	BSgenomeViews-class
getSeq,BSgenome-method	getSeq-methods
getSeq,XStringSet-method	getSeq-methods
granges,BSgenomeViews-method	BSgenomeViews-class
hasOnlyBaseLetters,BSgenomeViews-method	BSgenomeViews-class
injectSNPs	injectSNPs
injectSNPs,BSgenome-method	injectSNPs
InjectSNPsHandler	injectSNPs
InjectSNPsHandler-class	injectSNPs
installed.genomes	available.genomes
installed.SNPs	injectSNPs
length,BSgenome-method	BSgenome-class
length,BSgenomeViews-method	BSgenomeViews-class
letterFrequency,BSgenomeViews-method	BSgenomeViews-class
masknames	BSgenome-class
masknames,BSgenome-method	BSgenome-class
matchPWM,BSgenome-method	BSgenome-utils
mseqnames	BSgenome-class
mseqnames,BSgenome-method	BSgenome-class
names,BSgenome-method	BSgenome-class
names,BSgenomeViews-method	BSgenomeViews-class
nchar,BSgenomeViews-method	BSgenomeViews-class
newSNPlocs	SNPlocs-class
newXtraSNPlocs	XtraSNPlocs-class
nucleotideFrequencyAt,BSgenomeViews-method	BSgenomeViews-class
oligonucleotideFrequency,BSgenomeViews-method	BSgenomeViews-class
organism,SNPlocs-method	SNPlocs-class
organism,XtraSNPlocs-method	XtraSNPlocs-class
provider,SNPlocs-method	SNPlocs-class
provider,XtraSNPlocs-method	XtraSNPlocs-class
providerVersion,SNPlocs-method	SNPlocs-class
providerVersion,XtraSNPlocs-method	XtraSNPlocs-class
ranges,BSgenomeViews-method	BSgenomeViews-class
referenceGenome	SNPlocs-class
referenceGenome,SNPlocs-method	SNPlocs-class
referenceGenome,XtraSNPlocs-method	XtraSNPlocs-class
releaseDate,SNPlocs-method	SNPlocs-class
releaseDate,XtraSNPlocs-method	XtraSNPlocs-class
releaseName,SNPlocs-method	SNPlocs-class
releaseName,XtraSNPlocs-method	XtraSNPlocs-class
seqinfo,BSgenome-method	BSgenome-class
seqinfo,BSgenomeViews-method	BSgenomeViews-class
seqinfo,SNPlocs-method	SNPlocs-class
seqinfo,XtraSNPlocs-method	XtraSNPlocs-class
seqinfo<-,BSgenome-method	BSgenome-class
seqnames,BSgenomeViews-method	BSgenomeViews-class
seqnames,SNPlocs-method	SNPlocs-class
seqnames,XtraSNPlocs-method	XtraSNPlocs-class
seqnames<-,BSgenome-method	BSgenome-class
seqtype,BSgenomeViews-method	BSgenomeViews-class
show,BSgenome-method	BSgenome-class
show,BSgenomeViews-method	BSgenomeViews-class
show,SNPlocs-method	SNPlocs-class
show,XtraSNPlocs-method	XtraSNPlocs-class
SNPcount	injectSNPs
snpcount	SNPlocs-class
SNPcount,BSgenome-method	injectSNPs
snpcount,BSgenome-method	injectSNPs
SNPcount,InjectSNPsHandler-method	injectSNPs
snpcount,InjectSNPsHandler-method	injectSNPs
snpcount,SNPlocs-method	SNPlocs-class
snpcount,XtraSNPlocs-method	XtraSNPlocs-class
snpid2alleles	SNPlocs-class
snpid2alleles,SNPlocs-method	SNPlocs-class
snpid2grange	SNPlocs-class
snpid2grange,SNPlocs-method	SNPlocs-class
snpid2loc	SNPlocs-class
snpid2loc,SNPlocs-method	SNPlocs-class
SNPlocs	SNPlocs-class
snplocs	SNPlocs-class
SNPlocs,BSgenome-method	injectSNPs
snplocs,BSgenome-method	injectSNPs
SNPlocs,InjectSNPsHandler-method	injectSNPs
snplocs,InjectSNPsHandler-method	injectSNPs
snplocs,SNPlocs-method	SNPlocs-class
SNPlocs-class	SNPlocs-class
SNPlocs_pkgname	injectSNPs
SNPlocs_pkgname,BSgenome-method	injectSNPs
SNPlocs_pkgname,InjectSNPsHandler-method	injectSNPs
snpsById	SNPlocs-class
snpsById,SNPlocs-method	SNPlocs-class
snpsById,XtraSNPlocs-method	XtraSNPlocs-class
snpsByOverlaps	SNPlocs-class
snpsByOverlaps,SNPlocs-method	SNPlocs-class
snpsByOverlaps,XtraSNPlocs-method	XtraSNPlocs-class
snpsBySeqname	SNPlocs-class
snpsBySeqname,SNPlocs-method	SNPlocs-class
snpsBySeqname,XtraSNPlocs-method	XtraSNPlocs-class
sourceUrl	BSgenome-class
sourceUrl,BSgenome-method	BSgenome-class
species,SNPlocs-method	SNPlocs-class
species,XtraSNPlocs-method	XtraSNPlocs-class
start,BSgenomeViews-method	BSgenomeViews-class
strand,BSgenomeViews-method	BSgenomeViews-class
subject,BSgenomeViews-method	BSgenomeViews-class
uniqueLetters,BSgenomeViews-method	BSgenomeViews-class
unlist,BSgenomeViews-method	BSgenomeViews-class
vcountPattern,BSgenome-method	BSgenome-utils
vcountPDict,BSgenome-method	BSgenome-utils
Views,BSgenome-method	BSgenomeViews-class
vmatchPattern,BSgenome-method	BSgenome-utils
vmatchPDict,BSgenome-method	BSgenome-utils
width,BSgenomeViews-method	BSgenomeViews-class
writeBSgenomeToFasta	export-methods
writeBSgenomeToTwobit	export-methods
XtraSNPlocs	XtraSNPlocs-class
XtraSNPlocs-class	XtraSNPlocs-class
[[,BSgenome-method	BSgenome-class