$,BSgenome-method	BSgenome-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
BSParams	BSParams-class
BSParams-class	BSParams-class
class:BSgenome	BSgenome-class
class:BSgenomeDataPkgSeed	BSgenomeForge
class:BSParams	BSParams-class
class:InjectSNPsHandler	injectSNPs
class:SNPlocs	SNPlocs-class
coerce,GenomeData,data.frame-method	GenomeData-class
coerce,GenomeData,RangedData-method	GenomeData-class
coerce,GenomeData,RangesList-method	GenomeData-class
coerce,GenomeDataList,data.frame-method	GenomeDataList-class
compatibleGenomes	SNPlocs-class
compatibleGenomes,SNPlocs-method	SNPlocs-class
countPWM,BSgenome-method	BSgenome-utils
export,BSgenome,FastaFile,ANY-method	export-methods
export,BSgenome,TwoBitFile,ANY-method	export-methods
export-methods	export-methods
forgeBSgenomeDataPkg	BSgenomeForge
forgeBSgenomeDataPkg,BSgenomeDataPkgSeed-method	BSgenomeForge
forgeBSgenomeDataPkg,character-method	BSgenomeForge
forgeBSgenomeDataPkg,list-method	BSgenomeForge
forgeMasksFiles	BSgenomeForge
forgeSeqFiles	BSgenomeForge
forgeSeqlengthsFile	BSgenomeForge
gdapply	gdapply
gdapply,GenomeData,function-method	gdapply
gdapply,GenomeDataList,function-method	gdapply
gdReduce	gdReduce
gdReduce,GenomeData-method	gdReduce
gdReduce,GenomeDataList-method	gdReduce
GenomeData	GenomeData-class
GenomeData-class	GenomeData-class
GenomeDataList	GenomeDataList-class
GenomeDataList-class	GenomeDataList-class
getBSgenome	available.genomes
getSeq,BSgenome-method	getSeq-methods
injectSNPs	injectSNPs
injectSNPs,BSgenome-method	injectSNPs
InjectSNPsHandler	injectSNPs
InjectSNPsHandler-class	injectSNPs
installed.genomes	available.genomes
installed.SNPs	injectSNPs
length,BSgenome-method	BSgenome-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
newSNPlocs	SNPlocs-class
organism,GenomeData-method	GenomeData-class
organism,SNPlocs-method	SNPlocs-class
provider,GenomeData-method	GenomeData-class
provider,SNPlocs-method	SNPlocs-class
providerVersion,GenomeData-method	GenomeData-class
providerVersion,SNPlocs-method	SNPlocs-class
referenceGenome	SNPlocs-class
referenceGenome,SNPlocs-method	SNPlocs-class
releaseDate,SNPlocs-method	SNPlocs-class
releaseName,SNPlocs-method	SNPlocs-class
seqinfo,BSgenome-method	BSgenome-class
seqinfo,SNPlocs-method	SNPlocs-class
seqinfo<-,BSgenome-method	BSgenome-class
seqnames,SNPlocs-method	SNPlocs-class
seqnames<-,BSgenome-method	BSgenome-class
show,BSgenome-method	BSgenome-class
show,GenomeData-method	GenomeData-class
show,SNPlocs-method	SNPlocs-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
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
sourceUrl	BSgenome-class
sourceUrl,BSgenome-method	BSgenome-class
species,SNPlocs-method	SNPlocs-class
vcountPattern,BSgenome-method	BSgenome-utils
vcountPDict,BSgenome-method	BSgenome-utils
vmatchPattern,BSgenome-method	BSgenome-utils
vmatchPDict,BSgenome-method	BSgenome-utils
[[,BSgenome-method	BSgenome-class
[[<-,BSgenome-method	BSgenome-class
