$,Quickload-method	Quickload-class
$,TrackDb-method	TrackDb-class
$<-,TrackDb-method	TrackDb-class
2BitFile	TwoBitFile-class
2BitFile-class	TwoBitFile-class
activeView	activeView-methods
activeView,BrowserSession-method	activeView-methods
activeView,UCSCView-method	activeView-methods
activeView-methods	activeView-methods
activeView<-	activeView-methods
activeView<--methods	activeView-methods
as.character,RTLFile-method	RTLFile-class
asBED	asBED
asBED,GAlignments-method	asBED
asBED,GRangesList-method	asBED
asGFF	asGFF
asGFF,GRangesList-method	asGFF
BasicTrackLine-class	basicTrackLine-class
BED15File	BEDFile-class
BED15File-class	BEDFile-class
Bed15TrackLine-class	Bed15TrackLine-class
BEDFile	BEDFile-class
BEDFile-class	BEDFile-class
BEDGraphFile	BEDFile-class
BEDGraphFile-class	BEDFile-class
BEDPEFile	BEDFile-class
BEDPEFile-class	BEDFile-class
BigWigFile	BigWigFile
BigWigFile-class	BigWigFile
BigWigFileList	BigWigFile
BigWigFileList-class	BigWigFile
BigWigSelection	BigWigSelection-class
BigWigSelection-class	BigWigSelection-class
blocks	blocks-methods
blocks,GenomicRanges-method	blocks-methods
blocks-methods	blocks-methods
BroadPeakFile	BEDFile-class
BroadPeakFile-class	BEDFile-class
browseGenome	browseGenome
browseGenome,GenomicRanges_OR_GenomicRangesList-method	browseGenome
browseGenome,missing-method	browseGenome
browserSession	browserSession-methods
browserSession,BrowserView-method	browserSession-methods
browserSession,character-method	browserSession-methods
browserSession,missing-method	browserSession-methods
browserSession,UCSCTableQuery-method	UCSCTableQuery-class
BrowserSession-class	browserSession-class
browserSession-methods	browserSession-methods
browserSession<-	UCSCTableQuery-class
browserSession<-,UCSCTableQuery,UCSCSession-method	UCSCTableQuery-class
browserView	browserView-methods
browserView,UCSCSession-method	browserView-methods
BrowserView-class	browserView-class
browserView-methods	browserView-methods
BrowserViewList	BrowserViewList-class
BrowserViewList-class	BrowserViewList-class
browserViews	browserViews-methods
browserViews,UCSCSession-method	browserViews-methods
browserViews-methods	browserViews-methods
BWFile	BigWigFile
BWFile-class	BigWigFile
Chain-class	Chain-class
ChainBlock-class	Chain-class
ChainFile	Chain-class
ChainFile-class	Chain-class
chrom	GenomicData
chrom,GRanges-method	GenomicData
chrom,IntegerRangesList-method	IntegerRangesList-methods
chrom<-	GenomicData
chrom<-,GRanges-method	GenomicData
chrom<-,IntegerRangesList-method	IntegerRangesList-methods
class:2BitFile	TwoBitFile-class
class:BED15File	BEDFile-class
class:BEDFile	BEDFile-class
class:BEDGraphFile	BEDFile-class
class:BigWigFile	BigWigFile
class:BigWigFileList	BigWigFile
class:BroadPeakFile	BEDFile-class
class:BWFile	BigWigFile
class:Chain	Chain-class
class:ChainBlock	Chain-class
class:ChainFile	Chain-class
class:CompressedFile	RTLFile-class
class:FastaFile	FastaFile-class
class:GFF1File	GFFFile-class
class:GFF2File	GFFFile-class
class:GFF3File	GFFFile-class
class:GFFFile	GFFFile-class
class:GTFFile	GFFFile-class
class:GVFFile	GFFFile-class
class:NarrowPeakFile	BEDFile-class
class:Quickload	Quickload-class
class:QuickloadGenome	QuickloadGenome-class
class:RTLFile	RTLFile-class
class:TrackDb	TrackDb-class
class:TwoBitFile	TwoBitFile-class
class:UCSCFile	UCSCFile-class
class:WIGFile	WIGFile-class
cleanupBigWigCache	BigWigFile
coerce,BasicTrackLine,character-method	basicTrackLine-class
coerce,BasicTrackLine,GraphTrackLine-method	wigTrackLine-class
coerce,Bed15TrackLine,character-method	Bed15TrackLine-class
coerce,character,BasicTrackLine-method	basicTrackLine-class
coerce,character,Bed15TrackLine-method	Bed15TrackLine-class
coerce,character,GraphTrackLine-method	wigTrackLine-class
coerce,character,Quickload-method	Quickload-class
coerce,character,TrackLine-method	ucscTrackLine-class
coerce,GenomicRanges,BigWigSelection-method	BigWigSelection-class
coerce,GRanges,UCSCData-method	UCSCData-class
coerce,GraphTrackLine,BasicTrackLine-method	wigTrackLine-class
coerce,GraphTrackLine,character-method	wigTrackLine-class
coerce,IntegerRangesList,BigWigSelection-method	BigWigSelection-class
coerce,TrackLine,character-method	ucscTrackLine-class
coerce,UCSCData,GRanges-method	UCSCData-class
CompressedFile-class	RTLFile-class
cpneTrack	cpneTrack
export	export
export,ANY,BamFile,ANY-method	BamFile-methods
export,ANY,BEDFile,ANY-method	BEDFile-class
export,ANY,BEDPEFile,ANY-method	BEDFile-class
export,ANY,BigWigFile,ANY-method	BigWigFile
export,ANY,character,character-method	export
export,ANY,character,missing-method	export
export,ANY,CompressedFile,missing-method	export
export,ANY,connection,character-method	export
export,ANY,connection,missing-method	export
export,ANY,FastaFile,ANY-method	FastaFile-class
export,ANY,GFFFile,ANY-method	GFFFile-class
export,ANY,missing,character-method	export
export,ANY,TabSeparatedFile,ANY-method	TabixFile-methods
export,ANY,TwoBitFile,ANY-method	TwoBitFile-class
export,ANY,UCSCFile,ANY-method	UCSCFile-class
export,ANY,WIGFile,ANY-method	WIGFile-class
export,DNAStringSet,character,ANY-method	TwoBitFile-class
export,DNAStringSet,TwoBitFile,ANY-method	TwoBitFile-class
export,GAlignmentPairs,BamFile,ANY-method	BamFile-methods
export,GAlignments,BamFile,ANY-method	BamFile-methods
export,GenomicRanges,BED15File,ANY-method	BEDFile-class
export,GenomicRanges,BEDFile,ANY-method	BEDFile-class
export,GenomicRanges,BigWigFile,ANY-method	BigWigFile
export,GenomicRanges,GFFFile,ANY-method	GFFFile-class
export,GenomicRanges,TabSeparatedFile,ANY-method	TabixFile-methods
export,GenomicRanges,UCSCFile,ANY-method	UCSCFile-class
export,GenomicRanges,WIGFile,ANY-method	WIGFile-class
export,GenomicRangesList,BEDFile,ANY-method	BEDFile-class
export,GenomicRangesList,GFFFile,ANY-method	GFFFile-class
export,GenomicRangesList,UCSCFile,ANY-method	UCSCFile-class
export,GenomicRangesList,WIGFile,ANY-method	WIGFile-class
export,GRangesList,BEDFile,ANY-method	BEDFile-class
export,GRangesList,GFFFile,ANY-method	GFFFile-class
export,GRangesList,GTFFile,ANY-method	GFFFile-class
export,List,BigWigFile,ANY-method	BigWigFile
export,Pairs,BEDPEFile,ANY-method	BEDFile-class
export,UCSCData,BED15File,ANY-method	BEDFile-class
export,UCSCData,BEDFile,ANY-method	BEDFile-class
export,UCSCData,UCSCFile,ANY-method	UCSCFile-class
export,UCSCData,WIGFile,ANY-method	WIGFile-class
export,XStringSet,FastaFile,ANY-method	FastaFile-class
export.2bit	TwoBitFile-class
export.2bit,ANY-method	TwoBitFile-class
export.bed	BEDFile-class
export.bed,ANY-method	BEDFile-class
export.bed,UCSCData,characterORconnection-method	UCSCData-class
export.bed15	BEDFile-class
export.bed15,ANY-method	BEDFile-class
export.bed15,UCSCData-method	UCSCData-class
export.bedGraph	BEDFile-class
export.bedGraph,ANY-method	BEDFile-class
export.bw	BigWigFile
export.bw,ANY-method	BigWigFile
export.gff	GFFFile-class
export.gff,ANY-method	GFFFile-class
export.gff,UCSCData,characterORconnection-method	UCSCData-class
export.gff1	GFFFile-class
export.gff1,ANY-method	GFFFile-class
export.gff2	GFFFile-class
export.gff2,ANY-method	GFFFile-class
export.gff3	GFFFile-class
export.gff3,ANY-method	GFFFile-class
export.ucsc	UCSCFile-class
export.ucsc,ANY,ANY-method	UCSCFile-class
export.ucsc,ANY,RTLFile-method	UCSCFile-class
export.ucsc,UCSCData,characterORconnection-method	UCSCData-class
export.wig	WIGFile-class
export.wig,ANY-method	WIGFile-class
exportToTabix	TabixFile-methods
exportToTabix,ANY,character-method	TabixFile-methods
FastaFile	FastaFile-class
FastaFile-class	FastaFile-class
FileForFormat	RTLFile-class
formatDescription	UCSCSchema-class
formatDescription,UCSCSchema-method	UCSCSchema-class
genome,BrowserSession-method	browserSession-class
genome,GFFFile-method	GFFFile-class
genome,Quickload-method	Quickload-class
genome,QuickloadGenome-method	QuickloadGenome-class
genome,ucscCart-method	ucscSession-class
genome,UCSCSchema-method	UCSCSchema-class
genome,UCSCSession-method	ucscSession-class
genome<-,BrowserSession-method	browserSession-class
genome<-,UCSCSession-method	ucscSession-class
genomeBrowsers	genomeBrowsers
GenomicData	GenomicData
GenomicRanges_OR_GenomicRangesList-class	browseGenome
GenomicSelection	GenomicSelection
getSeq,TwoBitFile-method	TwoBitFile-class
getTable	UCSCTableQuery-class
getTable,UCSCSession-method	ucscSession-class
getTable,UCSCTableQuery-method	UCSCTableQuery-class
GFF1File	GFFFile-class
GFF1File-class	GFFFile-class
GFF2File	GFFFile-class
GFF2File-class	GFFFile-class
GFF3File	GFFFile-class
GFF3File-class	GFFFile-class
GFFcolnames	readGFF
GFFFile	GFFFile-class
GFFFile-class	GFFFile-class
GRangesForBSGenome	GRangesForUCSCGenome
GRangesForUCSCGenome	GRangesForUCSCGenome
GraphTrackLine-class	wigTrackLine-class
GTFFile	GFFFile-class
GTFFile-class	GFFFile-class
GVFFile	GFFFile-class
GVFFile-class	GFFFile-class
import	export
import,BamFile,ANY,ANY-method	BamFile-methods
import,BED15File,ANY,ANY-method	BEDFile-class
import,BEDFile,ANY,ANY-method	BEDFile-class
import,BEDPEFile,ANY,ANY-method	BEDFile-class
import,BigWigFile,ANY,ANY-method	BigWigFile
import,BroadPeakFile,ANY,ANY-method	BEDFile-class
import,BroadPeakFile,ANY-method	BEDFile-class
import,ChainFile,ANY,ANY-method	Chain-class
import,character,character,ANY-method	export
import,character,missing,ANY-method	export
import,CompressedFile,missing,ANY-method	export
import,connection,character,ANY-method	export
import,connection,missing,ANY-method	export
import,FastaFile,ANY,ANY-method	FastaFile-class
import,GFFFile,ANY,ANY-method	GFFFile-class
import,missing,ANY,character-method	export
import,NarrowPeakFile,ANY,ANY-method	BEDFile-class
import,NarrowPeakFile,ANY-method	BEDFile-class
import,TabixFile,ANY,ANY-method	TabixFile-methods
import,TwoBitFile,ANY,ANY-method	TwoBitFile-class
import,UCSCFile,ANY,ANY-method	UCSCFile-class
import,WIGFile,ANY,ANY-method	WIGFile-class
import.2bit	TwoBitFile-class
import.2bit,ANY-method	TwoBitFile-class
import.bed	BEDFile-class
import.bed,ANY-method	BEDFile-class
import.bed15	BEDFile-class
import.bed15,ANY-method	BEDFile-class
import.bedGraph	BEDFile-class
import.bedGraph,ANY-method	BEDFile-class
import.BroadPeak	BEDFile-class
import.BroadPeak,ANY-method	BEDFile-class
import.bw	BigWigFile
import.bw,ANY-method	BigWigFile
import.chain	Chain-class
import.chain,ANY-method	Chain-class
import.gff	GFFFile-class
import.gff,ANY-method	GFFFile-class
import.gff1	GFFFile-class
import.gff1,ANY-method	GFFFile-class
import.gff2	GFFFile-class
import.gff2,ANY-method	GFFFile-class
import.gff3	GFFFile-class
import.gff3,ANY-method	GFFFile-class
import.NarrowPeak	BEDFile-class
import.NarrowPeak,ANY-method	BEDFile-class
import.ucsc	UCSCFile-class
import.ucsc,ANY-method	UCSCFile-class
import.ucsc,RTLFile-method	UCSCFile-class
import.wig	WIGFile-class
import.wig,ANY-method	WIGFile-class
initialize,UCSCData-method	UCSCData-class
initialize,UCSCSession-method	ucscSession-class
IntegerRangesList-methods	IntegerRangesList-methods
length,Quickload-method	Quickload-class
length,QuickloadGenome-method	QuickloadGenome-class
liftOver	liftOver
liftOver,ANY,ANY-method	liftOver
liftOver,GenomicRanges,Chain-method	liftOver
mcols,QuickloadGenome-method	QuickloadGenome-class
names,BrowserSession-method	browserSession-class
names,QuickloadGenome-method	QuickloadGenome-class
names,UCSCTableQuery-method	UCSCTableQuery-class
names<-,UCSCTableQuery-method	UCSCTableQuery-class
NarrowPeakFile	BEDFile-class
NarrowPeakFile-class	BEDFile-class
nrow,UCSCSchema-method	UCSCSchema-class
offset,ChainBlock-method	Chain-class
organism,QuickloadGenome-method	QuickloadGenome-class
path	RTLFile-class
path,BigWigFileList-method	BigWigFile
path,RTLFile-method	RTLFile-class
Quickload	Quickload-class
quickload	QuickloadGenome-class
Quickload-class	Quickload-class
QuickloadGenome	QuickloadGenome-class
QuickloadGenome-class	QuickloadGenome-class
range,BrowserSession-method	browserSession-class
range,ucscCart-method	ucscSession-class
range,UCSCSession-method	ucscSession-class
range,UCSCTableQuery-method	UCSCTableQuery-class
range,UCSCView-method	ucscView-class
range<-	ucscSession-class
range<-,UCSCSession-method	ucscSession-class
range<-,UCSCTableQuery-method	UCSCTableQuery-class
range<-,UCSCView-method	ucscView-class
ranges,ChainBlock-method	Chain-class
readGFF	readGFF
referenceSequence	QuickloadGenome-class
referenceSequence,QuickloadGenome-method	QuickloadGenome-class
referenceSequence<-	QuickloadGenome-class
referenceSequence<-,QuickloadGenome-method	QuickloadGenome-class
releaseDate,QuickloadGenome-method	QuickloadGenome-class
resource	RTLFile-class
reversed	Chain-class
reversed,ChainBlock-method	Chain-class
RTLFile-class	RTLFile-class
RTLFileList-class	RTLFile-class
score,ANY-method	GenomicData
score,ChainBlock-method	Chain-class
seqinfo,BigWigFile-method	BigWigFile
seqinfo,DNAStringSet-method	QuickloadGenome-class
seqinfo,QuickloadGenome-method	QuickloadGenome-class
seqinfo,TwoBitFile-method	TwoBitFile-class
seqinfo,UCSCSession-method	ucscSession-class
seqinfo<-,QuickloadGenome-method	QuickloadGenome-class
SeqinfoForBSGenome	GRangesForUCSCGenome
SeqinfoForUCSCGenome	GRangesForUCSCGenome
sequence<-	laySequence-methods
sequence<--methods	laySequence-methods
show,BrowserSession-method	browserSession-class
show,BrowserView-method	browserView-class
show,Quickload-method	Quickload-class
show,QuickloadGenome-method	QuickloadGenome-class
show,RTLFile-method	RTLFile-class
show,TrackLine-method	ucscTrackLine-class
show,UCSCData-method	UCSCData-class
show,UCSCTableQuery-method	UCSCTableQuery-class
space,ChainBlock-method	Chain-class
split,UCSCData,ANY-method	UCSCData-class
split,UCSCData,Vector-method	UCSCData-class
summary,BigWigFile-method	BigWigFile
tableName	UCSCTableQuery-class
tableName,UCSCSchema-method	UCSCSchema-class
tableName,UCSCTableQuery-method	UCSCTableQuery-class
tableName<-	UCSCTableQuery-class
tableName<-,UCSCTableQuery-method	UCSCTableQuery-class
tableNames	UCSCTableQuery-class
tableNames,UCSCTableQuery-method	UCSCTableQuery-class
targets	targets
track	UCSCTableQuery-class
track,QuickloadGenome-method	QuickloadGenome-class
track,UCSCSession-method	ucscSession-class
track,UCSCTableQuery-method	UCSCTableQuery-class
track<-	layTrack-methods
track<-,BrowserSession,ANY-method	layTrack-methods
track<-,QuickloadGenome,ANY-method	QuickloadGenome-class
track<-,QuickloadGenome,character-method	QuickloadGenome-class
track<-,QuickloadGenome,RsamtoolsFile-method	QuickloadGenome-class
track<-,QuickloadGenome,RTLFile-method	QuickloadGenome-class
track<-,TrackDb,ANY-method	TrackDb-class
track<-,UCSCSession,GenomicRangesList-method	ucscSession-class
track<-,UCSCSession,RTLFile-method	ucscSession-class
track<--methods	layTrack-methods
TrackDb-class	TrackDb-class
TrackLine-class	ucscTrackLine-class
trackName	UCSCTableQuery-class
trackName,UCSCTableQuery-method	UCSCTableQuery-class
trackName<-	UCSCTableQuery-class
trackName<-,UCSCTableQuery-method	UCSCTableQuery-class
trackNames	tracks-methods
trackNames,BrowserSession-method	browserSession-class
trackNames,UCSCSession-method	tracks-methods
trackNames,UCSCTableQuery-method	UCSCTableQuery-class
trackNames,UCSCTrackModes-method	tracks-methods
trackNames,UCSCView-method	tracks-methods
trackNames-methods	tracks-methods
trackNames<-	tracks-methods
trackNames<-,UCSCTrackModes-method	tracks-methods
trackNames<-,UCSCView-method	tracks-methods
trackNames<--methods	tracks-methods
TwoBitFile	TwoBitFile-class
TwoBitFile-class	TwoBitFile-class
UCSCData-class	UCSCData-class
UCSCFile	UCSCFile-class
UCSCFile-class	UCSCFile-class
ucscGenomes	ucscGenomes
ucscSchema	UCSCTableQuery-class
ucscSchema,UCSCSchemaDescription-method	UCSCSchema-class
ucscSchema,UCSCTableQuery-method	UCSCTableQuery-class
UCSCSchema-class	UCSCSchema-class
UCSCSession-class	ucscSession-class
ucscTableQuery	UCSCTableQuery-class
ucscTableQuery,UCSCSession-method	UCSCTableQuery-class
UCSCTableQuery-class	UCSCTableQuery-class
ucscTrackModes	ucscTrackModes-methods
ucscTrackModes,character-method	ucscTrackModes-methods
ucscTrackModes,missing-method	ucscTrackModes-methods
ucscTrackModes,UCSCSession-method	ucscTrackModes-methods
ucscTrackModes,ucscTracks-method	ucscTrackModes-methods
ucscTrackModes,UCSCView-method	ucscTrackModes-methods
UCSCTrackModes-class	ucscTrackModes-class
ucscTrackModes-methods	ucscTrackModes-methods
ucscTrackModes<-	ucscTrackModes-methods
ucscTrackModes<-,UCSCView,character-method	ucscTrackModes-methods
ucscTrackModes<-,UCSCView,UCSCTrackModes-method	ucscTrackModes-methods
ucscTrackModes<--methods	ucscTrackModes-methods
UCSCView-class	ucscView-class
uri	Quickload-class
uri,QuickloadGenome-method	QuickloadGenome-class
viewURL	ucscView-class
visible	browserView-class
visible,BrowserView-method	browserView-class
visible,UCSCView-method	ucscView-class
visible<-	browserView-class
visible<-,BrowserView-method	browserView-class
visible<-,UCSCView-method	ucscView-class
WIGFile	WIGFile-class
WIGFile-class	WIGFile-class
wigToBigWig	wigToBigWig
[,UCSCTrackModes,ANY,ANY,ANY-method	ucscTrackModes-class
[<-,UCSCTrackModes,ANY,ANY,ANY-method	ucscTrackModes-class
[[,Quickload,ANY,ANY-method	Quickload-class
[[,TrackDb,ANY,ANY-method	TrackDb-class
[[<-,TrackDb,ANY,ANY-method	TrackDb-class
