!,CompressedLogicalList-method	AtomicList-class
!,CompressedRleList-method	AtomicList-class
!,Rle-method	Rle-class
!,SimpleLogicalList-method	AtomicList-class
!,SimpleRleList-method	AtomicList-class
!=	Ranges-comparison
!=,integer,XIntegerViews-method	XIntegerViews-class
!=,Ranges,Ranges-method	Ranges-comparison
!=,Sequence,Sequence-method	Sequence-class
!=,SharedVector,SharedVector-method	IRanges-internals
!=,XInteger,XIntegerViews-method	XIntegerViews-class
!=,XIntegerViews,integer-method	XIntegerViews-class
!=,XIntegerViews,XInteger-method	XIntegerViews-class
!=,XIntegerViews,XIntegerViews-method	XIntegerViews-class
$,Sequence-method	Sequence-class
$<-,CompressedList-method	SimpleList-class
$<-,RangedData-method	RangedData-class
$<-,SimpleList-method	SimpleList-class
%in%,CompressedAtomicList,atomic-method	AtomicList-class
%in%,CompressedAtomicList,AtomicList-method	AtomicList-class
%in%,CompressedRleList,atomic-method	AtomicList-class
%in%,CompressedRleList,AtomicList-method	AtomicList-class
%in%,RangedData,RangedData-method	IntervalTree-class
%in%,RangedData,RangesList-method	IntervalTree-class
%in%,Ranges,Ranges-method	IntervalTree-class
%in%,RangesList,RangedData-method	IntervalTree-class
%in%,RangesList,RangesList-method	IntervalTree-class
%in%,Rle,ANY-method	Rle-class
%in%,SimpleAtomicList,atomic-method	AtomicList-class
%in%,SimpleAtomicList,AtomicList-method	AtomicList-class
%in%,SimpleRleList,atomic-method	AtomicList-class
%in%,SimpleRleList,AtomicList-method	AtomicList-class
<	Ranges-comparison
<,Ranges,Ranges-method	Ranges-comparison
<=	Ranges-comparison
<=,Ranges,Ranges-method	Ranges-comparison
==	Ranges-comparison
==,integer,XIntegerViews-method	XIntegerViews-class
==,Ranges,Ranges-method	Ranges-comparison
==,SharedVector,SharedVector-method	IRanges-internals
==,XDouble,XDouble-method	XVector-class
==,XInteger,XInteger-method	XVector-class
==,XInteger,XIntegerViews-method	XIntegerViews-class
==,XIntegerViews,integer-method	XIntegerViews-class
==,XIntegerViews,XInteger-method	XIntegerViews-class
==,XIntegerViews,XIntegerViews-method	XIntegerViews-class
>	Ranges-comparison
>,Ranges,Ranges-method	Ranges-comparison
>=	Ranges-comparison
>=,Ranges,Ranges-method	Ranges-comparison
active	MaskCollection-class
active,FilterRules-method	FilterRules-class
active,MaskCollection-method	MaskCollection-class
active<-	MaskCollection-class
active<-,FilterRules-method	FilterRules-class
active<-,MaskCollection-method	MaskCollection-class
aggregate,CompressedList-method	SimpleList-class
aggregate,data.frame-method	Sequence-class
aggregate,DataTable-method	DataTable-class
aggregate,matrix-method	Sequence-class
aggregate,Rle-method	Rle-class
aggregate,Sequence-method	Sequence-class
aggregate,SimpleList-method	SimpleList-class
aggregate,ts-method	Sequence-class
aggregate,vector-method	Sequence-class
Annotated	Annotated-class
Annotated-class	Annotated-class
append,FilterRules,FilterRules-method	FilterRules-class
append,MaskCollection,MaskCollection-method	MaskCollection-class
append,Sequence,Sequence-method	Sequence-class
applyFun	RDApplyParams-class
applyFun,RDApplyParams-method	RDApplyParams-class
applyFun<-	RDApplyParams-class
applyFun<-,RDApplyParams-method	RDApplyParams-class
applyParams	RDApplyParams-class
applyParams,RDApplyParams-method	RDApplyParams-class
applyParams<-	RDApplyParams-class
applyParams<-,RDApplyParams-method	RDApplyParams-class
as.character,AtomicList-method	AtomicList-class
as.character,Rle-method	Rle-class
as.complex,AtomicList-method	AtomicList-class
as.complex,Rle-method	Rle-class
as.data.frame,AtomicList-method	AtomicList-class
as.data.frame,DataFrame-method	DataFrame-class
as.data.frame,DataFrameList-method	DataFrameList-class
as.data.frame,GappedRanges-method	GappedRanges-class
as.data.frame,GroupedIRanges-method	XVectorList-class
as.data.frame,RangedData-method	RangedData-class
as.data.frame,Ranges-method	Ranges-class
as.data.frame,RangesList-method	RangesList-class
as.data.frame,Rle-method	Rle-class
as.env	Sequence-class
as.env,DataTable-method	DataTable-class
as.env,RangedData-method	RangedData-class
as.env,Sequence-method	Sequence-class
as.factor,AtomicList-method	AtomicList-class
as.factor,Rle-method	Rle-class
as.integer,AtomicList-method	AtomicList-class
as.integer,Ranges-method	Ranges-class
as.integer,Rle-method	Rle-class
as.integer,SharedInteger-method	IRanges-internals
as.integer,SharedRaw-method	IRanges-internals
as.integer,XInteger-method	XVector-class
as.integer,XRaw-method	XVector-class
as.list,CompressedAtomicList-method	AtomicList-class
as.list,CompressedList-method	SimpleList-class
as.list,CompressedNormalIRangesList-method	IRangesList-class
as.list,Sequence-method	Sequence-class
as.list,SimpleList-method	SimpleList-class
as.logical,AtomicList-method	AtomicList-class
as.logical,Rle-method	Rle-class
as.matrix,Ranges-method	Ranges-class
as.matrix,RangesMatching-method	RangesMatching-class
as.matrix,RangesMatchingList-method	RangesMatchingList-class
as.numeric,AtomicList-method	AtomicList-class
as.numeric,Rle-method	Rle-class
as.numeric,SharedDouble-method	IRanges-internals
as.numeric,SharedVector-method	IRanges-internals
as.numeric,XDouble-method	XVector-class
as.numeric,XVector-method	XVector-class
as.raw,AtomicList-method	AtomicList-class
as.raw,Rle-method	Rle-class
as.raw,XRaw-method	XVector-class
as.table,RangesMatching-method	RangesMatching-class
as.table,RangesMatchingList-method	RangesMatchingList-class
as.vector,AtomicList,missing-method	AtomicList-class
as.vector,Rle,missing-method	Rle-class
as.vector,XDouble,missing-method	XVector-class
as.vector,XInteger,missing-method	XVector-class
as.vector,XRaw,missing-method	XVector-class
asNormalIRanges	IRanges-utils
AtomicList-class	AtomicList-class
Binning	Grouping-class
Binning-class	Grouping-class
by,DataTable-method	DataTable-class
c,CompressedList-method	SimpleList-class
c,FilterRules-method	FilterRules-class
c,GappedRanges-method	GappedRanges-class
c,GroupedIRanges-method	XVectorList-class
c,IRanges-method	IRanges-class
c,RangedData-method	RangedData-class
c,Rle-method	Rle-class
c,Sequence-method	Sequence-class
c,SharedVector_Pool-method	IRanges-internals
c,SimpleList-method	SimpleList-class
c,XRaw-method	XVector-class
c,XVectorList-method	XVectorList-class
cbind	DataTable-class
cbind,DataFrame-method	DataFrame-class
cbind,DataFrameList-method	DataFrameList-class
cbind,DataTable-method	DataTable-class
CharacterList	AtomicList-class
CharacterList-class	AtomicList-class
characterORNULL	IRanges-internals
characterORNULL-class	IRanges-internals
chartr,ANY,ANY,CompressedCharacterList-method	AtomicList-class
chartr,ANY,ANY,CompressedRleList-method	AtomicList-class
chartr,ANY,ANY,Rle-method	Rle-class
chartr,ANY,ANY,SimpleCharacterList-method	AtomicList-class
chartr,ANY,ANY,SimpleRleList-method	AtomicList-class
class:Binning	Grouping-class
class:characterORNULL	IRanges-internals
class:CompressedIRangesList	IRangesList-class
class:CompressedNormalIRangesList	IRangesList-class
class:DataTable	DataTable-class
class:Dups	Grouping-class
class:GappedRanges	GappedRanges-class
class:GroupedIRanges	XVectorList-class
class:Grouping	Grouping-class
class:H2LGrouping	Grouping-class
class:IRanges	IRanges-class
class:IRangesList	IRangesList-class
class:MaskCollection	MaskCollection-class
class:NormalIRanges	IRanges-class
class:NormalIRangesList	IRangesList-class
class:Partitioning	Grouping-class
class:PartitioningByEnd	Grouping-class
class:PartitioningByWidth	Grouping-class
class:Ranges	Ranges-class
class:RangesList-class	RangesList-class
class:Rle	Rle-class
class:RleViews	RleViews-class
class:Sequence	Sequence-class
class:SharedDouble	IRanges-internals
class:SharedInteger	IRanges-internals
class:SharedRaw	IRanges-internals
class:SharedRaw_Pool	IRanges-internals
class:SharedVector	IRanges-internals
class:SharedVector_Pool	IRanges-internals
class:SimpleIRangesList	IRangesList-class
class:SimpleNormalIRangesList	IRangesList-class
class:SimpleRangesList-class	RangesList-class
class:Views	Views-class
class:XDouble	XVector-class
class:XInteger	XVector-class
class:XIntegerViews	XIntegerViews-class
class:XRaw	XVector-class
class:XRawList	XVectorList-class
class:XVector	XVector-class
class:XVectorList	XVectorList-class
coerce,ANY,CompressedSplitDataFrameList-method	DataFrameList-class
coerce,ANY,SimpleSplitDataFrameList-method	DataFrameList-class
coerce,ANY,vector-method	IRanges-internals
coerce,AtomicList,character-method	AtomicList-class
coerce,AtomicList,complex-method	AtomicList-class
coerce,AtomicList,data.frame-method	AtomicList-class
coerce,AtomicList,factor-method	AtomicList-class
coerce,AtomicList,integer-method	AtomicList-class
coerce,AtomicList,logical-method	AtomicList-class
coerce,AtomicList,numeric-method	AtomicList-class
coerce,AtomicList,raw-method	AtomicList-class
coerce,AtomicList,vector-method	AtomicList-class
coerce,character,Rle-method	Rle-class
coerce,complex,Rle-method	Rle-class
coerce,CompressedAtomicList,list-method	AtomicList-class
coerce,CompressedIRangesList,CompressedNormalIRangesList-method	IRangesList-class
coerce,CompressedIRangesList,GappedRanges-method	GappedRanges-class
coerce,CompressedNormalIRangesList,GappedRanges-method	GappedRanges-class
coerce,data.frame,DataFrame-method	DataFrame-class
coerce,data.frame,RangedData-method	RangedData-class
coerce,DataFrame,data.frame-method	DataFrame-class
coerce,DataFrameList,DataFrame-method	DataFrameList-class
coerce,DataTable,RangedData-method	RangedData-class
coerce,factor,Rle-method	Rle-class
coerce,GappedRanges,CompressedIRangesList-method	GappedRanges-class
coerce,GappedRanges,CompressedNormalIRangesList-method	GappedRanges-class
coerce,GappedRanges,IRangesList-method	GappedRanges-class
coerce,GappedRanges,NormalIRangesList-method	GappedRanges-class
coerce,GappedRanges,RangesList-method	GappedRanges-class
coerce,integer,DataFrame-method	DataFrame-class
coerce,integer,IRanges-method	IRanges-class
coerce,integer,NormalIRanges-method	IRanges-class
coerce,integer,Rle-method	Rle-class
coerce,integer,XVector-method	XVector-class
coerce,IntervalTree,IRanges-method	IntervalTree-class
coerce,IRanges,IntervalTree-method	IntervalTree-class
coerce,IRanges,NormalIRanges-method	IRanges-utils
coerce,list,DataFrame-method	DataFrame-class
coerce,logical,IRanges-method	IRanges-class
coerce,logical,NormalIRanges-method	IRanges-class
coerce,logical,Rle-method	Rle-class
coerce,LogicalList,CompressedIRangesList-method	AtomicList-class
coerce,LogicalList,CompressedNormalIRangesList-method	AtomicList-class
coerce,LogicalList,IRangesList-method	AtomicList-class
coerce,LogicalList,NormalIRangesList-method	AtomicList-class
coerce,LogicalList,SimpleIRangesList-method	AtomicList-class
coerce,LogicalList,SimpleNormalIRangesList-method	AtomicList-class
coerce,MaskCollection,NormalIRanges-method	MaskCollection-class
coerce,matrix,DataFrame-method	DataFrame-class
coerce,NULL,DataFrame-method	DataFrame-class
coerce,numeric,IRanges-method	IRanges-class
coerce,numeric,NormalIRanges-method	IRanges-class
coerce,numeric,Rle-method	Rle-class
coerce,numeric,XDouble-method	XVector-class
coerce,numeric,XInteger-method	XVector-class
coerce,numeric,XRaw-method	XVector-class
coerce,numeric,XVector-method	XVector-class
coerce,RangedData,DataFrame-method	RangedData-class
coerce,Ranges,IntervalTree-method	IntervalTree-class
coerce,Ranges,IRanges-method	IRanges-class
coerce,Ranges,PartitioningByEnd-method	Grouping-class
coerce,Ranges,PartitioningByWidth-method	Grouping-class
coerce,Ranges,RangedData-method	RangedData-class
coerce,RangesList,CompressedIRangesList-method	RangesList-class
coerce,RangesList,CompressedNormalIRangesList-method	RangesList-class
coerce,RangesList,IRangesList-method	RangesList-class
coerce,RangesList,NormalIRangesList-method	RangesList-class
coerce,RangesList,RangedData-method	RangesList-class
coerce,RangesList,RangedSelection-method	RangedSelection-class
coerce,RangesList,SimpleIRangesList-method	RangesList-class
coerce,RangesList,SimpleNormalIRangesList-method	RangesList-class
coerce,raw,Rle-method	Rle-class
coerce,raw,XRaw-method	XVector-class
coerce,raw,XVector-method	XVector-class
coerce,Rle,character-method	Rle-class
coerce,Rle,complex-method	Rle-class
coerce,Rle,data.frame-method	Rle-class
coerce,Rle,factor-method	Rle-class
coerce,Rle,integer-method	Rle-class
coerce,Rle,IRanges-method	Rle-class
coerce,Rle,logical-method	Rle-class
coerce,Rle,NormalIRanges-method	Rle-class
coerce,Rle,numeric-method	Rle-class
coerce,Rle,RangedData-method	RangedData-class
coerce,Rle,raw-method	Rle-class
coerce,Rle,vector-method	Rle-class
coerce,RleList,CompressedIRangesList-method	AtomicList-class
coerce,RleList,CompressedNormalIRangesList-method	AtomicList-class
coerce,RleList,IRangesList-method	AtomicList-class
coerce,RleList,NormalIRangesList-method	AtomicList-class
coerce,RleList,RangedData-method	RangedData-class
coerce,RleList,SimpleIRangesList-method	AtomicList-class
coerce,RleList,SimpleNormalIRangesList-method	AtomicList-class
coerce,RleViewsList,CompressedIRangesList-method	RleViewsList-class
coerce,RleViewsList,IRangesList-method	RleViewsList-class
coerce,RleViewsList,SimpleIRangesList-method	RleViewsList-class
coerce,Sequence,CompressedSplitDataFrameList-method	DataFrameList-class
coerce,Sequence,DataFrame-method	DataFrame-class
coerce,Sequence,list-method	Sequence-class
coerce,Sequence,SimpleSplitDataFrameList-method	DataFrameList-class
coerce,Sequence,Views-method	Views-class
coerce,SharedVector,SharedVector_Pool-method	IRanges-internals
coerce,SimpleIRangesList,SimpleNormalIRangesList-method	IRangesList-class
coerce,SplitDataFrameList,DataFrame-method	DataFrameList-class
coerce,table,DataFrame-method	DataFrame-class
coerce,vector,AtomicList-method	AtomicList-class
coerce,vector,DataFrame-method	DataFrame-class
coerce,vector,Rle-method	Rle-class
coerce,Views,NormalIRanges-method	Views-class
collapse	MaskCollection-class
collapse,MaskCollection-method	MaskCollection-class
colnames,CompressedSplitDataFrameList-method	DataFrameList-class
colnames,DataFrame-method	DataFrame-class
colnames,DataFrameList-method	DataFrameList-class
colnames,RangedData-method	RangedData-class
colnames,RangedSelection-method	RangedSelection-class
colnames,SimpleSplitDataFrameList-method	DataFrameList-class
colnames<-,CompressedSplitDataFrameList-method	DataFrameList-class
colnames<-,DataFrame-method	DataFrame-class
colnames<-,RangedData-method	RangedData-class
colnames<-,RangedSelection-method	RangedSelection-class
colnames<-,SimpleDataFrameList-method	DataFrameList-class
columnMetadata	DataFrameList-class
columnMetadata,CompressedSplitDataFrameList-method	DataFrameList-class
columnMetadata,RangedData-method	RangedData-class
columnMetadata,SimpleSplitDataFrameList-method	DataFrameList-class
columnMetadata<-	DataFrameList-class
columnMetadata<-,CompressedSplitDataFrameList-method	DataFrameList-class
columnMetadata<-,RangedData-method	RangedData-class
columnMetadata<-,SimpleSplitDataFrameList-method	DataFrameList-class
complete.cases,DataTable-method	DataTable-class
Complex,CompressedAtomicList-method	AtomicList-class
Complex,Rle-method	Rle-class
Complex,SimpleAtomicList-method	AtomicList-class
ComplexList	AtomicList-class
ComplexList-class	AtomicList-class
CompressedAtomicList-class	AtomicList-class
CompressedCharacterList	AtomicList-class
CompressedCharacterList-class	AtomicList-class
CompressedComplexList	AtomicList-class
CompressedComplexList-class	AtomicList-class
CompressedIntegerList	AtomicList-class
CompressedIntegerList-class	AtomicList-class
CompressedIRangesList	IRangesList-class
CompressedIRangesList-class	IRangesList-class
CompressedList	SimpleList-class
CompressedList-class	SimpleList-class
CompressedLogicalList	AtomicList-class
CompressedLogicalList-class	AtomicList-class
CompressedNormalIRangesList	IRangesList-class
CompressedNormalIRangesList-class	IRangesList-class
CompressedNumericList	AtomicList-class
CompressedNumericList-class	AtomicList-class
CompressedRawList	AtomicList-class
CompressedRawList-class	AtomicList-class
CompressedRleList	AtomicList-class
CompressedRleList-class	AtomicList-class
CompressedSplitDataFrameList-class	DataFrameList-class
cor,IntegerList,AtomicList-method	AtomicList-class
cor,LogicalList,AtomicList-method	AtomicList-class
cor,NumericList,AtomicList-method	AtomicList-class
cor,Rle,Rle-method	Rle-class
cor,RleList,AtomicList-method	AtomicList-class
countOverlap	IntervalTree-class
countOverlaps	IntervalTree-class
countOverlaps,RangedData,RangedData-method	IntervalTree-class
countOverlaps,RangedData,RangesList-method	IntervalTree-class
countOverlaps,Ranges,Ranges-method	IntervalTree-class
countOverlaps,RangesList,RangedData-method	IntervalTree-class
countOverlaps,RangesList,RangesList-method	IntervalTree-class
cov,IntegerList,AtomicList-method	AtomicList-class
cov,LogicalList,AtomicList-method	AtomicList-class
cov,NumericList,AtomicList-method	AtomicList-class
cov,Rle,Rle-method	Rle-class
cov,RleList,AtomicList-method	AtomicList-class
coverage	coverage
coverage,IRanges-method	coverage
coverage,MaskCollection-method	coverage
coverage,numeric-method	coverage
coverage,RangedData-method	coverage
coverage,RangesList-method	coverage
coverage,Views-method	coverage
coverage.normargWidth	coverage
DataFrame	DataFrame-class
DataFrame-class	DataFrame-class
DataFrameList	DataFrameList-class
DataFrameList-class	DataFrameList-class
DataTable	DataTable-class
DataTable-class	DataTable-class
DataTable-stats	DataTable-stats
DataTableORNULL-class	DataTable-class
desc	MaskCollection-class
desc,MaskCollection-method	MaskCollection-class
desc<-	MaskCollection-class
desc<-,MaskCollection-method	MaskCollection-class
diff,IntegerList-method	AtomicList-class
diff,NumericList-method	AtomicList-class
diff,Rle-method	Rle-class
diff,RleList-method	AtomicList-class
dim,DataFrameList-method	DataFrameList-class
dim,DataTable-method	DataTable-class
dim,RangesMatching-method	RangesMatching-class
dimnames,DataFrameList-method	DataFrameList-class
dimnames,DataTable-method	DataTable-class
dimnames<-,DataFrameList-method	DataFrameList-class
dimnames<-,DataTable-method	DataTable-class
disjoin	disjoin
disjoin,Ranges-method	disjoin
disjoin,RangesList-method	RangesList-utils
disjointBins	disjoin
disjointBins,Ranges-method	disjoin
duplicated,Dups-method	Grouping-class
duplicated,Ranges-method	Ranges-comparison
Dups	Grouping-class
Dups-class	Grouping-class
elementLengths	Sequence-class
elementLengths,CompressedList-method	Sequence-class
elementLengths,GappedRanges-method	GappedRanges-class
elementLengths,list-method	Sequence-class
elementLengths,RangedData-method	RangedData-class
elementLengths,Ranges-method	Ranges-class
elementLengths,Sequence-method	Sequence-class
elementMetadata	Sequence-class
elementMetadata,Sequence-method	Sequence-class
elementMetadata<-	Sequence-class
elementMetadata<-,Sequence-method	Sequence-class
elementType	Sequence-class
elementType,Sequence-method	Sequence-class
elementType,vector-method	Sequence-class
end,CompressedIRangesList-method	IRangesList-class
end,GappedRanges-method	GappedRanges-class
end,IntervalTree-method	IntervalTree-class
end,PartitioningByEnd-method	Grouping-class
end,PartitioningByWidth-method	Grouping-class
end,RangedData-method	RangedData-class
end,Ranges-method	Ranges-class
end,RangesList-method	RangesList-class
end,Rle-method	Rle-class
end<-	Ranges-class
end<-,IRanges-method	IRanges-class
end<-,RangedData-method	RangedData-class
end<-,RangesList-method	RangesList-class
endoapply	endoapply
endoapply,CompressedList-method	SimpleList-class
endoapply,data.frame-method	endoapply
endoapply,list-method	endoapply
endoapply,RangedData-method	RangedData-class
endoapply,Sequence-method	Sequence-class
endoapply,SimpleList-method	SimpleList-class
eval,expressionORlanguage,Sequence-method	Sequence-class
eval,FilterRules,ANY-method	FilterRules-class
Filter,ANY,Sequence-method	Sequence-class
FilterRules	FilterRules-class
filterRules	RDApplyParams-class
filterRules,RDApplyParams-method	RDApplyParams-class
FilterRules-class	FilterRules-class
filterRules<-	RDApplyParams-class
filterRules<-,RDApplyParams-method	RDApplyParams-class
Find,ANY,Sequence-method	Sequence-class
findOverlaps	IntervalTree-class
findOverlaps,ANY,missing-method	IntervalTree-class
findOverlaps,integer,Ranges-method	IntervalTree-class
findOverlaps,RangedData,RangedData-method	IntervalTree-class
findOverlaps,RangedData,RangesList-method	IntervalTree-class
findOverlaps,Ranges,IntervalTree-method	IntervalTree-class
findOverlaps,Ranges,Ranges-method	IntervalTree-class
findOverlaps,RangesList,RangedData-method	IntervalTree-class
findOverlaps,RangesList,RangesList-method	IntervalTree-class
findRange	Rle-class
findRange,Rle-method	Rle-class
findRun	Rle-class
findRun,Rle-method	Rle-class
first	Ranges-class
first,Ranges-method	Ranges-class
flank	Ranges-utils
flank,CompressedIRangesList-method	RangesList-utils
flank,NormalIRanges-method	Ranges-utils
flank,Ranges-method	Ranges-utils
flank,RangesList-method	RangesList-utils
follow	nearest
follow,Ranges,RangesORmissing-method	nearest
GappedRanges	GappedRanges-class
GappedRanges-class	GappedRanges-class
gaps	IRanges-setops
gaps,CompressedIRangesList-method	RangesList-utils
gaps,IRanges-method	IRanges-setops
gaps,MaskCollection-method	MaskCollection-class
gaps,Ranges-method	IRanges-setops
gaps,RangesList-method	RangesList-utils
gaps,Views-method	Views-class
GroupedIRanges	XVectorList-class
GroupedIRanges-class	XVectorList-class
Grouping	Grouping-class
Grouping-class	Grouping-class
grouplength	Grouping-class
grouplength,Binning-method	Grouping-class
grouplength,Grouping-method	Grouping-class
grouplength,H2LGrouping-method	Grouping-class
grouplength,Partitioning-method	Grouping-class
grouprank	Grouping-class
grouprank,H2LGrouping-method	Grouping-class
gsub,ANY,ANY,CompressedCharacterList-method	AtomicList-class
gsub,ANY,ANY,CompressedRleList-method	AtomicList-class
gsub,ANY,ANY,Rle-method	Rle-class
gsub,ANY,ANY,SimpleCharacterList-method	AtomicList-class
gsub,ANY,ANY,SimpleRleList-method	AtomicList-class
H2LGrouping	Grouping-class
H2LGrouping-class	Grouping-class
head,DataTable-method	DataTable-class
head,Sequence-method	Sequence-class
high2low	Grouping-class
high2low,H2LGrouping-method	Grouping-class
high2low,Sequence-method	Grouping-class
high2low,vector-method	Grouping-class
IntegerList	AtomicList-class
IntegerList-class	AtomicList-class
intersect,IRanges,IRanges-method	IRanges-setops
intersect,RangesList,RangesList-method	RangesList-utils
IntervalTree	IntervalTree-class
IntervalTree-class	IntervalTree-class
IQR,IntegerList-method	AtomicList-class
IQR,LogicalList-method	AtomicList-class
IQR,NumericList-method	AtomicList-class
IQR,Rle-method	Rle-class
IQR,RleList-method	AtomicList-class
IRanges	IRanges-constructor
IRanges-class	IRanges-class
IRanges-constructor	IRanges-constructor
IRanges-setops	IRanges-setops
IRanges-utils	IRanges-utils
IRangesList	IRangesList-class
IRangesList-class	IRangesList-class
is.na,CompressedAtomicList-method	AtomicList-class
is.na,CompressedRleList-method	AtomicList-class
is.na,DataTable-method	DataTable-class
is.na,Rle-method	Rle-class
is.na,SimpleAtomicList-method	AtomicList-class
is.na,SimpleRleList-method	AtomicList-class
is.unsorted,Rle-method	Rle-class
isConstant	IRanges-internals
isDisjoint	Ranges-class
isDisjoint,Ranges-method	Ranges-class
isDisjoint,RangesList-method	IRangesList-class
isEmpty	Sequence-class
isEmpty,ANY-method	Sequence-class
isEmpty,CompressedList-method	SimpleList-class
isEmpty,NormalIRanges-method	IRanges-class
isEmpty,Ranges-method	Ranges-class
isEmpty,SimpleList-method	SimpleList-class
isNormal	Ranges-class
isNormal,CompressedIRangesList-method	IRangesList-class
isNormal,IRanges-method	IRanges-class
isNormal,Ranges-method	Ranges-class
isNormal,RangesList-method	IRangesList-class
isNormal,SimpleIRangesList-method	IRangesList-class
isSingleInteger	IRanges-internals
isSingleIntegerOrNA	IRanges-internals
isSingleNumber	IRanges-internals
isSingleNumberOrNA	IRanges-internals
isSingleString	IRanges-internals
isSingleStringOrNA	IRanges-internals
isTRUEorFALSE	IRanges-internals
lapply,CompressedAtomicList-method	AtomicList-class
lapply,CompressedList-method	SimpleList-class
lapply,RangedData-method	RangedData-class
lapply,Sequence-method	Sequence-class
lapply,SimpleList-method	SimpleList-class
last	Ranges-class
last,Ranges-method	Ranges-class
length,Binning-method	Grouping-class
length,CompressedList-method	SimpleList-class
length,GappedRanges-method	GappedRanges-class
length,H2LGrouping-method	Grouping-class
length,IntervalTree-method	IntervalTree-class
length,MaskCollection-method	MaskCollection-class
length,PartitioningByEnd-method	Grouping-class
length,PartitioningByWidth-method	Grouping-class
length,RangedData-method	RangedData-class
length,Ranges-method	Ranges-class
length,RangesMatching-method	RangesMatching-class
length,Rle-method	Rle-class
length,SharedVector-method	IRanges-internals
length,SharedVector_Pool-method	IRanges-internals
length,SimpleList-method	SimpleList-class
length,XVector-method	XVector-class
length,XVectorList-method	XVectorList-class
length<-,H2LGrouping-method	Grouping-class
levels,Rle-method	Rle-class
levels<-,Rle-method	Rle-class
LogicalList	AtomicList-class
LogicalList-class	AtomicList-class
low2high	Grouping-class
low2high,H2LGrouping-method	Grouping-class
mad,IntegerList-method	AtomicList-class
mad,LogicalList-method	AtomicList-class
mad,NumericList-method	AtomicList-class
mad,Rle-method	Rle-class
mad,RleList-method	AtomicList-class
Map	Sequence-class
Map,Sequence-method	Sequence-class
mapply	Sequence-class
mapply,Sequence-method	Sequence-class
Mask	MaskCollection-class
MaskCollection	MaskCollection-class
MaskCollection-class	MaskCollection-class
MaskCollection.show_frame	MaskCollection-class
maskedratio	MaskCollection-class
maskedratio,MaskCollection-method	MaskCollection-class
maskedwidth	MaskCollection-class
maskedwidth,MaskCollection-method	MaskCollection-class
match,CompressedAtomicList,atomic-method	AtomicList-class
match,CompressedAtomicList,AtomicList-method	AtomicList-class
match,CompressedRleList,atomic-method	AtomicList-class
match,CompressedRleList,AtomicList-method	AtomicList-class
match,RangedData,RangedData-method	IntervalTree-class
match,RangedData,RangesList-method	IntervalTree-class
match,Ranges,Ranges-method	IntervalTree-class
match,RangesList,RangedData-method	IntervalTree-class
match,RangesList,RangesList-method	IntervalTree-class
match,Rle,ANY-method	Rle-class
match,SimpleAtomicList,atomic-method	AtomicList-class
match,SimpleAtomicList,AtomicList-method	AtomicList-class
match,SimpleRleList,atomic-method	AtomicList-class
match,SimpleRleList,AtomicList-method	AtomicList-class
matchMatrix	RangesMatching-class
matchMatrix,RangesMatching-method	RangesMatching-class
Math,CompressedAtomicList-method	AtomicList-class
Math,Rle-method	Rle-class
Math,SimpleAtomicList-method	AtomicList-class
Math2,CompressedAtomicList-method	AtomicList-class
Math2,Rle-method	Rle-class
Math2,SimpleAtomicList-method	AtomicList-class
max,CompressedNormalIRangesList-method	IRangesList-class
max,MaskCollection-method	MaskCollection-class
max,NormalIRanges-method	IRanges-class
max,SimpleNormalIRangesList-method	IRangesList-class
mean,IntegerList-method	AtomicList-class
mean,LogicalList-method	AtomicList-class
mean,NumericList-method	AtomicList-class
mean,Rle-method	Rle-class
mean,RleList-method	AtomicList-class
median,IntegerList-method	AtomicList-class
median,LogicalList-method	AtomicList-class
median,NumericList-method	AtomicList-class
median,Rle-method	Rle-class
median,RleList-method	AtomicList-class
members	Grouping-class
members,Grouping-method	Grouping-class
members,H2LGrouping-method	Grouping-class
mendoapply	endoapply
mendoapply,CompressedList-method	SimpleList-class
mendoapply,data.frame-method	endoapply
mendoapply,list-method	endoapply
mendoapply,Sequence-method	Sequence-class
mendoapply,SimpleList-method	SimpleList-class
metadata	Annotated-class
metadata,Annotated-method	Annotated-class
metadata<-	Annotated-class
metadata<-,Annotated-method	Annotated-class
mid	Ranges-class
mid,Ranges-method	Ranges-class
min,CompressedNormalIRangesList-method	IRangesList-class
min,MaskCollection-method	MaskCollection-class
min,NormalIRanges-method	IRanges-class
min,SimpleNormalIRangesList-method	IRangesList-class
mseqapply	seqapply
na.exclude	DataTable-class
na.exclude,DataTable-method	DataTable-class
na.omit	DataTable-class
na.omit,DataTable-method	DataTable-class
names,Binning-method	Grouping-class
names,CompressedList-method	SimpleList-class
names,GappedRanges-method	GappedRanges-class
names,IRanges-method	IRanges-class
names,MaskCollection-method	MaskCollection-class
names,Partitioning-method	Grouping-class
names,RangedData-method	RangedData-class
names,SimpleList-method	SimpleList-class
names,XVectorList-method	XVectorList-class
names<-,Binning-method	Grouping-class
names<-,CompressedList-method	SimpleList-class
names<-,GappedRanges-method	GappedRanges-class
names<-,IRanges-method	IRanges-class
names<-,MaskCollection-method	MaskCollection-class
names<-,Partitioning-method	Grouping-class
names<-,RangedData-method	RangedData-class
names<-,SimpleList-method	SimpleList-class
names<-,XVectorList-method	XVectorList-class
narrow	Ranges-utils
narrow,CompressedIRangesList-method	RangesList-utils
narrow,NormalIRanges-method	Ranges-utils
narrow,Ranges-method	Ranges-utils
narrow,RangesList-method	RangesList-utils
narrow,XVectorList-method	XVectorList-class
nchar,CompressedCharacterList-method	AtomicList-class
nchar,CompressedRleList-method	AtomicList-class
nchar,Rle-method	Rle-class
nchar,SimpleCharacterList-method	AtomicList-class
nchar,SimpleRleList-method	AtomicList-class
ncol,CompressedSplitDataFrameList-method	DataFrameList-class
ncol,DataFrame-method	DataFrame-class
ncol,DataFrameList-method	DataFrameList-class
NCOL,DataTable-method	DataTable-class
ncol,RangedData-method	RangedData-class
ncol,SimpleSplitDataFrameList-method	DataFrameList-class
nearest	nearest
nearest,Ranges,RangesORmissing-method	nearest
new2	IRanges-internals
newViews	Views-class
ngap	GappedRanges-class
ngap,GappedRanges-method	GappedRanges-class
nir_list	MaskCollection-class
nir_list,MaskCollection-method	MaskCollection-class
nlevels,Sequence-method	Sequence-class
nobj	Grouping-class
nobj,Binning-method	Grouping-class
nobj,H2LGrouping-method	Grouping-class
nobj,PartitioningByEnd-method	Grouping-class
nobj,PartitioningByWidth-method	Grouping-class
NormalIRanges	IRanges-class
NormalIRanges-class	IRanges-class
NormalIRangesList	IRangesList-class
NormalIRangesList-class	IRangesList-class
normargShift	IRanges-internals
normargWeight	IRanges-internals
nrow,DataFrame-method	DataFrame-class
nrow,DataFrameList-method	DataFrameList-class
NROW,DataTable-method	DataTable-class
nrow,RangedData-method	RangedData-class
NROW,Sequence-method	Sequence-class
nrun	Rle-class
nrun,Rle-method	Rle-class
NumericList	AtomicList-class
NumericList-class	AtomicList-class
Ops,atomic,AtomicList-method	AtomicList-class
Ops,atomic,CompressedAtomicList-method	AtomicList-class
Ops,AtomicList,atomic-method	AtomicList-class
Ops,CompressedAtomicList,atomic-method	AtomicList-class
Ops,CompressedAtomicList,CompressedAtomicList-method	AtomicList-class
Ops,CompressedAtomicList,SimpleAtomicList-method	AtomicList-class
Ops,Ranges,numeric-method	Ranges-class
Ops,RangesList,ANY-method	RangesList-class
Ops,Rle,Rle-method	Rle-class
Ops,Rle,vector-method	Rle-class
Ops,SimpleAtomicList,CompressedAtomicList-method	AtomicList-class
Ops,SimpleAtomicList,SimpleAtomicList-method	AtomicList-class
Ops,vector,Rle-method	Rle-class
order	Ranges-comparison
order,Ranges-method	Ranges-comparison
overlap	IntervalTree-class
Partitioning	Grouping-class
Partitioning-class	Grouping-class
PartitioningByEnd	Grouping-class
PartitioningByEnd-class	Grouping-class
PartitioningByWidth	Grouping-class
PartitioningByWidth-class	Grouping-class
paste	Rle-class
paste,Rle-method	Rle-class
pgap	IRanges-setops
pgap,IRanges,IRanges-method	IRanges-setops
pintersect	IRanges-setops
pintersect,IRanges,IRanges-method	IRanges-setops
pmax	Rle-class
pmax,IntegerList-method	AtomicList-class
pmax,NumericList-method	AtomicList-class
pmax,Rle-method	Rle-class
pmax,RleList-method	AtomicList-class
pmax.int	Rle-class
pmax.int,IntegerList-method	AtomicList-class
pmax.int,NumericList-method	AtomicList-class
pmax.int,Rle-method	Rle-class
pmax.int,RleList-method	AtomicList-class
pmin	Rle-class
pmin,IntegerList-method	AtomicList-class
pmin,NumericList-method	AtomicList-class
pmin,Rle-method	Rle-class
pmin,RleList-method	AtomicList-class
pmin.int	Rle-class
pmin.int,IntegerList-method	AtomicList-class
pmin.int,NumericList-method	AtomicList-class
pmin.int,Rle-method	Rle-class
pmin.int,RleList-method	AtomicList-class
Position,ANY,Sequence-method	Sequence-class
precede	nearest
precede,Ranges,RangesORmissing-method	nearest
psetdiff	IRanges-setops
psetdiff,IRanges,IRanges-method	IRanges-setops
punion	IRanges-setops
punion,IRanges,IRanges-method	IRanges-setops
quantile,IntegerList-method	AtomicList-class
quantile,LogicalList-method	AtomicList-class
quantile,NumericList-method	AtomicList-class
quantile,Rle-method	Rle-class
quantile,RleList-method	AtomicList-class
queryHits	RangesMatching-class
queryHits,RangesMatching-method	RangesMatching-class
queryHits,RangesMatchingList-method	RangesMatchingList-class
range,IRanges-method	Ranges-utils
range,RangedData-method	RangedData-utils
range,Ranges-method	Ranges-utils
range,RangesList-method	RangesList-utils
RangedData	RangedData-class
rangedData	RDApplyParams-class
rangedData,RDApplyParams-method	RDApplyParams-class
RangedData-class	RangedData-class
RangedData-utils	RangedData-utils
rangedData<-	RDApplyParams-class
rangedData<-,RDApplyParams-method	RDApplyParams-class
RangedDataList	RangedDataList-class
RangedDataList-class	RangedDataList-class
RangedSelection	RangedSelection-class
RangedSelection-class	RangedSelection-class
Ranges	Ranges-class
ranges	RangedData-class
ranges,RangedData-method	RangedData-class
ranges,RangedSelection-method	RangedSelection-class
ranges,RangesMatching-method	RangesMatching-class
ranges,RangesMatchingList-method	RangesMatchingList-class
Ranges-class	Ranges-class
Ranges-comparison	Ranges-comparison
Ranges-utils	Ranges-utils
ranges<-	RangedData-class
ranges<-,RangedData-method	RangedData-class
ranges<-,RangedSelection-method	RangedSelection-class
RangesList	RangesList-class
RangesList-class	RangesList-class
RangesList-utils	RangesList-utils
RangesMatching-class	RangesMatching-class
RangesMatchingList-class	RangesMatchingList-class
RangesORmissing-class	Ranges-class
rank,Ranges-method	Ranges-comparison
RawList	AtomicList-class
RawList-class	AtomicList-class
rbind	DataTable-class
rbind,DataFrame-method	DataFrame-class
rbind,DataFrameList-method	DataFrameList-class
rbind,DataTable-method	DataTable-class
rbind,RangedData-method	RangedData-class
rdapply	RDApplyParams-class
rdapply,RDApplyParams-method	RDApplyParams-class
RDApplyParams	RDApplyParams-class
RDApplyParams-class	RDApplyParams-class
read.agpMask	read.Mask
read.gapMask	read.Mask
read.liftMask	read.Mask
read.Mask	read.Mask
read.rmMask	read.Mask
read.trfMask	read.Mask
reduce	Ranges-utils
Reduce,ANY,Sequence-method	Sequence-class
reduce,CompressedIRangesList-method	RangesList-utils
reduce,IRanges-method	Ranges-utils
reduce,RangedData-method	RangedData-class
reduce,Ranges-method	Ranges-utils
reduce,RangesList-method	RangesList-utils
reducerFun	RDApplyParams-class
reducerFun,RDApplyParams-method	RDApplyParams-class
reducerFun<-	RDApplyParams-class
reducerFun<-,RDApplyParams-method	RDApplyParams-class
reducerParams	RDApplyParams-class
reducerParams,RDApplyParams-method	RDApplyParams-class
reducerParams<-	RDApplyParams-class
reducerParams<-,RDApplyParams-method	RDApplyParams-class
reflect	Ranges-utils
reflect,NormalIRanges-method	Ranges-utils
reflect,Ranges-method	Ranges-utils
rep,Rle-method	Rle-class
rep,Sequence-method	Sequence-class
rep.int	Sequence-class
rep.int,Rle-method	Rle-class
rep.int,Sequence-method	Sequence-class
resize	Ranges-utils
resize,CompressedIRangesList-method	RangesList-utils
resize,NormalIRanges-method	Ranges-utils
resize,Ranges-method	Ranges-utils
resize,RangesList-method	RangesList-utils
restrict	Ranges-utils
restrict,CompressedIRangesList-method	RangesList-utils
restrict,NormalIRanges-method	Ranges-utils
restrict,Ranges-method	Ranges-utils
restrict,RangesList-method	RangesList-utils
rev,Rle-method	Rle-class
rev,Sequence-method	Sequence-class
reverse	reverse
reverse,IRanges-method	reverse
reverse,MaskCollection-method	reverse
reverse,NormalIRanges-method	reverse
reverse,SharedRaw-method	reverse
reverse,SharedVector_Pool-method	reverse
Rle	Rle-class
Rle,missing,missing-method	Rle-class
Rle,vectorORfactor,integer-method	Rle-class
Rle,vectorORfactor,missing-method	Rle-class
Rle,vectorORfactor,numeric-method	Rle-class
Rle-class	Rle-class
RleList	AtomicList-class
RleList-class	AtomicList-class
RleViews	RleViews-class
RleViews-class	RleViews-class
RleViewsList	RleViewsList-class
RleViewsList-class	RleViewsList-class
rownames,DataFrame-method	DataFrame-class
rownames,DataFrameList-method	DataFrameList-class
rownames,RangedData-method	RangedData-class
rownames<-,CompressedSplitDataFrameList-method	DataFrameList-class
rownames<-,DataFrame-method	DataFrame-class
rownames<-,RangedData-method	RangedData-class
rownames<-,SimpleDataFrameList-method	DataFrameList-class
runLength	Rle-class
runLength,Rle-method	Rle-class
runLength<-	Rle-class
runLength<-,Rle-method	Rle-class
runmean	runstat
runmean,Rle-method	Rle-class
runmean,RleList-method	AtomicList-class
runmed,CompressedIntegerList-method	AtomicList-class
runmed,NumericList-method	AtomicList-class
runmed,Rle-method	Rle-class
runmed,RleList-method	AtomicList-class
runmed,SimpleIntegerList-method	AtomicList-class
runq	runstat
runq,Rle-method	Rle-class
runq,RleList-method	AtomicList-class
runstat	runstat
runsum	runstat
runsum,Rle-method	Rle-class
runsum,RleList-method	AtomicList-class
runValue	Rle-class
runValue,Rle-method	Rle-class
runValue<-	Rle-class
runValue<-,Rle-method	Rle-class
runwtsum	runstat
runwtsum,Rle-method	Rle-class
runwtsum,RleList-method	AtomicList-class
safeExplode	strutils
sapply,Sequence-method	Sequence-class
score	score
score,AlignmentSpace-method	Alignment-class
score,RangedData-method	RangedData-class
score<-	score
score<-,RangedData-method	RangedData-class
sd,IntegerList-method	AtomicList-class
sd,LogicalList-method	AtomicList-class
sd,NumericList-method	AtomicList-class
sd,Rle-method	Rle-class
sd,RleList-method	AtomicList-class
seqapply	seqapply
seqselect	Sequence-class
seqselect,CompressedList-method	SimpleList-class
seqselect,DataFrame-method	DataFrame-class
seqselect,DataTable-method	DataTable-class
seqselect,factor-method	Sequence-class
seqselect,GappedRanges-method	GappedRanges-class
seqselect,GroupedIRanges-method	XVectorList-class
seqselect,IRanges-method	IRanges-class
seqselect,NULL-method	Sequence-class
seqselect,RangedData-method	RangedData-class
seqselect,Rle-method	Rle-class
seqselect,Sequence-method	Sequence-class
seqselect,SimpleList-method	SimpleList-class
seqselect,vector-method	Sequence-class
seqselect,XVector-method	XVector-class
seqselect,XVectorList-method	XVectorList-class
seqselect<-	Sequence-class
seqselect<-,CompressedAtomicList-method	AtomicList-class
seqselect<-,CompressedList-method	SimpleList-class
seqselect<-,DataTable-method	DataTable-class
seqselect<-,factor-method	Sequence-class
seqselect<-,IRanges-method	IRanges-class
seqselect<-,RangedData-method	RangedData-class
seqselect<-,Rle-method	Rle-class
seqselect<-,Sequence-method	Sequence-class
seqselect<-,SimpleAtomicList-method	AtomicList-class
seqselect<-,SimpleList-method	SimpleList-class
seqselect<-,vector-method	Sequence-class
seqsplit	seqapply
Sequence	Sequence-class
Sequence-class	Sequence-class
setdiff,IRanges,IRanges-method	IRanges-setops
setdiff,RangesList,RangesList-method	RangesList-utils
setValidity2	IRanges-internals
SharedDouble	IRanges-internals
SharedDouble-class	IRanges-internals
SharedInteger	IRanges-internals
SharedInteger-class	IRanges-internals
SharedRaw	IRanges-internals
SharedRaw-class	IRanges-internals
SharedRaw.read	IRanges-internals
SharedRaw.readComplexes	IRanges-internals
SharedRaw.readInts	IRanges-internals
SharedRaw.write	IRanges-internals
SharedRaw.writeInts	IRanges-internals
SharedRaw_Pool-class	IRanges-internals
SharedVector	IRanges-internals
SharedVector-class	IRanges-internals
SharedVector.compare	IRanges-internals
SharedVector.copy	IRanges-internals
SharedVector_Pool-class	IRanges-internals
shift	Ranges-utils
shift,CompressedIRangesList-method	RangesList-utils
shift,Ranges-method	Ranges-utils
shift,RangesList-method	RangesList-utils
shiftApply	Sequence-class
shiftApply,Rle,Rle-method	Rle-class
shiftApply,Sequence,Sequence-method	Sequence-class
shiftApply,vector,vector-method	Sequence-class
show,AtomicList-method	AtomicList-class
show,CompressedList-method	SimpleList-class
show,DataTable-method	DataTable-class
show,Dups-method	Grouping-class
show,externalptr-method	IRanges-internals
show,GappedRanges-method	GappedRanges-class
show,GroupedIRanges-method	XVectorList-class
show,Grouping-method	Grouping-class
show,IRangesList-method	IRangesList-class
show,MaskCollection-method	MaskCollection-class
show,RangedData-method	RangedData-class
show,Ranges-method	Ranges-class
show,RangesList-method	RangesList-class
show,Rle-method	Rle-class
show,RleList-method	AtomicList-class
show,RleViews-method	RleViews-class
show,SharedDouble-method	IRanges-internals
show,SharedInteger-method	IRanges-internals
show,SharedVector-method	IRanges-internals
show,SharedVector_Pool-method	IRanges-internals
show,SimpleList-method	SimpleList-class
show,SplitDataFrameList-method	DataFrameList-class
show,XDouble-method	XVector-class
show,XIntegerViews-method	XIntegerViews-class
show,XVector-method	XVector-class
SimpleAtomicList-class	AtomicList-class
SimpleCharacterList	AtomicList-class
SimpleCharacterList-class	AtomicList-class
SimpleComplexList	AtomicList-class
SimpleComplexList-class	AtomicList-class
SimpleDataFrameList-class	DataFrameList-class
SimpleIntegerList	AtomicList-class
SimpleIntegerList-class	AtomicList-class
SimpleIRangesList	IRangesList-class
SimpleIRangesList-class	IRangesList-class
SimpleList	SimpleList-class
SimpleList-class	SimpleList-class
SimpleLogicalList	AtomicList-class
SimpleLogicalList-class	AtomicList-class
SimpleNormalIRangesList	IRangesList-class
SimpleNormalIRangesList-class	IRangesList-class
SimpleNumericList	AtomicList-class
SimpleNumericList-class	AtomicList-class
SimpleRangesList	RangesList-class
SimpleRangesList-class	RangesList-class
SimpleRawList	AtomicList-class
SimpleRawList-class	AtomicList-class
SimpleRleList	AtomicList-class
SimpleRleList-class	AtomicList-class
SimpleRleViewsList-class	RleViewsList-class
SimpleSplitDataFrameList-class	DataFrameList-class
simplify	RDApplyParams-class
simplify,RDApplyParams-method	RDApplyParams-class
simplify<-	RDApplyParams-class
simplify<-,RDApplyParams-method	RDApplyParams-class
slice	Views-utils
slice,integer-method	Views-utils
slice,Rle-method	Views-utils
slice,RleList-method	Views-utils
slice,XInteger-method	Views-utils
smoothEnds,CompressedIntegerList-method	AtomicList-class
smoothEnds,NumericList-method	AtomicList-class
smoothEnds,Rle-method	Rle-class
smoothEnds,RleList-method	AtomicList-class
smoothEnds,SimpleIntegerList-method	AtomicList-class
solveUserSEW	IRanges-constructor
solveUserSEW0	IRanges-constructor
sort,AtomicList-method	AtomicList-class
sort,Ranges-method	Ranges-comparison
sort,Rle-method	Rle-class
space	RangesList-class
space,RangedData-method	RangedData-class
space,RangesList-method	RangesList-class
space,RangesMatchingList-method	RangesMatchingList-class
split,DataFrame-method	DataFrame-class
split,IRanges-method	IRangesList-class
split,RangedData-method	RangedData-class
split,Ranges-method	RangesList-class
split,Rle-method	Rle-class
SplitDataFrameList	DataFrameList-class
SplitDataFrameList-class	DataFrameList-class
splitRanges	Rle-class
splitRanges,Rle-method	Rle-class
splitRanges,vectorORfactor-method	Rle-class
stack,DataFrameList-method	DataFrameList-class
stack,RangedDataList-method	RangedDataList-class
stack,Sequence-method	Sequence-class
start,CompressedIRangesList-method	IRangesList-class
start,GappedRanges-method	GappedRanges-class
start,IntervalTree-method	IntervalTree-class
start,IRanges-method	IRanges-class
start,PartitioningByEnd-method	Grouping-class
start,PartitioningByWidth-method	Grouping-class
start,RangedData-method	RangedData-class
start,Ranges-method	Ranges-class
start,RangesList-method	RangesList-class
start,Rle-method	Rle-class
start<-	Ranges-class
start<-,IRanges-method	IRanges-class
start<-,RangedData-method	RangedData-class
start<-,RangesList-method	RangesList-class
strsplitAsListOfIntegerVectors	strutils
sub,ANY,ANY,CompressedCharacterList-method	AtomicList-class
sub,ANY,ANY,CompressedRleList-method	AtomicList-class
sub,ANY,ANY,Rle-method	Rle-class
sub,ANY,ANY,SimpleCharacterList-method	AtomicList-class
sub,ANY,ANY,SimpleRleList-method	AtomicList-class
subject	Views-class
subject,SimpleRleViewsList-method	RleViewsList-class
subject,Views-method	Views-class
subjectHits	RangesMatching-class
subjectHits,RangesMatching-method	RangesMatching-class
subjectHits,RangesMatchingList-method	RangesMatchingList-class
subseq	XVector-class
subseq,MaskCollection-method	MaskCollection-class
subseq,XVector-method	XVector-class
subseq,XVectorList-method	XVectorList-class
subseq<-	XVector-class
subseq<-,XVector-method	XVector-class
subset,DataTable-method	DataTable-class
subset,Sequence-method	Sequence-class
subsetByOverlaps	IntervalTree-class
subsetByOverlaps,RangedData,RangedData-method	IntervalTree-class
subsetByOverlaps,RangedData,RangesList-method	IntervalTree-class
subsetByOverlaps,Ranges,Ranges-method	IntervalTree-class
subsetByOverlaps,RangesList,RangedData-method	IntervalTree-class
subsetByOverlaps,RangesList,RangesList-method	IntervalTree-class
substr,Rle-method	Rle-class
substring,Rle-method	Rle-class
subviews	Views-class
subviews,Views-method	Views-class
successiveIRanges	IRanges-utils
successiveViews	Views-class
Summary,AtomicList-method	AtomicList-class
summary,CompressedIRangesList-method	IRangesList-class
Summary,Rle-method	Rle-class
summary,Rle-method	Rle-class
svn.time	strutils
t,RangesMatching-method	RangesMatching-class
t,RangesMatchingList-method	RangesMatchingList-class
table	Rle-class
table,CompressedAtomicList-method	AtomicList-class
table,Rle-method	Rle-class
table,SimpleAtomicList-method	AtomicList-class
tail,DataTable-method	DataTable-class
tail,Sequence-method	Sequence-class
tapply,Sequence-method	Sequence-class
threebands	Ranges-utils
threebands,IRanges-method	Ranges-utils
threebands,XVectorList-method	XVectorList-class
togroup	Grouping-class
togroup,Binning-method	Grouping-class
togroup,H2LGrouping-method	Grouping-class
togroup,Partitioning-method	Grouping-class
togrouplength	Grouping-class
togrouplength,Grouping-method	Grouping-class
togrouprank	Grouping-class
togrouprank,H2LGrouping-method	Grouping-class
tolower,CompressedCharacterList-method	AtomicList-class
tolower,CompressedRleList-method	AtomicList-class
tolower,Rle-method	Rle-class
tolower,SimpleCharacterList-method	AtomicList-class
tolower,SimpleRleList-method	AtomicList-class
toString,SharedRaw-method	IRanges-internals
toupper,CompressedCharacterList-method	AtomicList-class
toupper,CompressedRleList-method	AtomicList-class
toupper,Rle-method	Rle-class
toupper,SimpleCharacterList-method	AtomicList-class
toupper,SimpleRleList-method	AtomicList-class
trim	Views-class
trim,Views-method	Views-class
tseqapply	seqapply
union,IRanges,IRanges-method	IRanges-setops
union,RangesList,RangesList-method	RangesList-utils
unique,AtomicList-method	AtomicList-class
unique,CompressedRleList-method	AtomicList-class
unique,Ranges-method	Ranges-comparison
unique,Rle-method	Rle-class
unique,SimpleRleList-method	AtomicList-class
universe	RangesList-class
universe,RangedData-method	RangedData-class
universe,RangesList-method	RangesList-class
universe<-	RangesList-class
universe<-,RangedData-method	RangedData-class
universe<-,RangesList-method	RangesList-class
unlist,CompressedList-method	SimpleList-class
unlist,IRangesList-method	IRangesList-class
unlist,RangedDataList-method	RangedDataList-class
unlist,Ranges-method	Ranges-class
unlist,SimpleList-method	SimpleList-class
unlist,SimpleNormalIRangesList-method	IRangesList-class
update,IRanges-method	IRanges-class
update,Ranges-method	Ranges-class
updateObject	updateObject
updateObject,AnnotatedList-method	updateObject
updateObject,ANY-method	updateObject
updateObject,CharacterList-method	updateObject
updateObject,ComplexList-method	updateObject
updateObject,FilterRules-method	updateObject
updateObject,IntegerList-method	updateObject
updateObject,IntervalTree-method	updateObject
updateObject,IRanges-method	updateObject
updateObject,IRangesList-method	updateObject
updateObject,LogicalList-method	updateObject
updateObject,MaskCollection-method	updateObject
updateObject,NormalIRanges-method	updateObject
updateObject,NumericList-method	updateObject
updateObject,RangedData-method	updateObject
updateObject,RangedDataList-method	updateObject
updateObject,RangesList-method	updateObject
updateObject,RangesMatchingList-method	updateObject
updateObject,RawList-method	updateObject
updateObject,RDApplyParams-method	updateObject
updateObject,Rle-method	updateObject
updateObject,RleList-method	updateObject
updateObject,RleViews-method	updateObject
updateObject,SplitXDataFrameList-method	updateObject
updateObject,XDataFrame-method	updateObject
updateObject,XDataFrameList-method	updateObject
updateObject,XIntegerViews-method	updateObject
updateObject,XVector-method	updateObject
values	Sequence-class
values,RangedData-method	RangedData-class
values,Sequence-method	Sequence-class
values<-	Sequence-class
values<-,RangedData-method	RangedData-class
values<-,Sequence-method	Sequence-class
var,IntegerList,AtomicList-method	AtomicList-class
var,IntegerList,missing-method	AtomicList-class
var,LogicalList,AtomicList-method	AtomicList-class
var,LogicalList,missing-method	AtomicList-class
var,NumericList,AtomicList-method	AtomicList-class
var,NumericList,missing-method	AtomicList-class
var,Rle,missing-method	Rle-class
var,Rle,Rle-method	Rle-class
var,RleList,AtomicList-method	AtomicList-class
var,RleList,missing-method	AtomicList-class
viewApply	Views-utils
viewApply,RleViews-method	Views-utils
viewApply,RleViewsList-method	Views-utils
viewApply,Views-method	Views-utils
viewMaxs	Views-utils
viewMaxs,RleViews-method	Views-utils
viewMaxs,RleViewsList-method	Views-utils
viewMaxs,XIntegerViews-method	Views-utils
viewMeans	Views-utils
viewMeans,RleViews-method	Views-utils
viewMeans,RleViewsList-method	Views-utils
viewMeans,XIntegerViews-method	Views-utils
viewMins	Views-utils
viewMins,RleViews-method	Views-utils
viewMins,RleViewsList-method	Views-utils
viewMins,XIntegerViews-method	Views-utils
viewRangeMaxs	Views-utils
viewRangeMaxs,RleViews-method	Views-utils
viewRangeMaxs,RleViewsList-method	Views-utils
viewRangeMins	Views-utils
viewRangeMins,RleViews-method	Views-utils
viewRangeMins,RleViewsList-method	Views-utils
Views	Views-class
views	Views-class
Views,integer-method	XIntegerViews-class
Views,Rle-method	RleViews-class
Views,RleList-method	RleViewsList-class
Views,XInteger-method	XIntegerViews-class
Views-class	Views-class
Views-utils	Views-utils
viewSums	Views-utils
viewSums,RleViews-method	Views-utils
viewSums,RleViewsList-method	Views-utils
viewSums,XIntegerViews-method	Views-utils
viewWhichMaxs	Views-utils
viewWhichMaxs,RleViews-method	Views-utils
viewWhichMaxs,RleViewsList-method	Views-utils
viewWhichMaxs,XIntegerViews-method	Views-utils
viewWhichMins	Views-utils
viewWhichMins,RleViews-method	Views-utils
viewWhichMins,RleViewsList-method	Views-utils
viewWhichMins,XIntegerViews-method	Views-utils
vmembers	Grouping-class
vmembers,Grouping-method	Grouping-class
vmembers,H2LGrouping-method	Grouping-class
which,CompressedLogicalList-method	AtomicList-class
which,CompressedRleList-method	AtomicList-class
which,Rle-method	Rle-class
which,SimpleLogicalList-method	AtomicList-class
which,SimpleRleList-method	AtomicList-class
whichAsIRanges	IRanges-utils
whichFirstNotNormal	Ranges-class
whichFirstNotNormal,Ranges-method	Ranges-class
whichFirstNotNormal,RangesList-method	IRangesList-class
width	Ranges-class
width,CompressedIRangesList-method	IRangesList-class
width,IRanges-method	IRanges-class
width,MaskCollection-method	MaskCollection-class
width,PartitioningByEnd-method	Grouping-class
width,PartitioningByWidth-method	Grouping-class
width,RangedData-method	RangedData-class
width,Ranges-method	Ranges-class
width,RangesList-method	RangesList-class
width,Rle-method	Rle-class
width,SharedVector_Pool-method	IRanges-internals
width,XVectorList-method	XVectorList-class
width<-	Ranges-class
width<-,IRanges-method	IRanges-class
width<-,RangedData-method	RangedData-class
width<-,RangesList-method	RangesList-class
window,DataTable-method	DataTable-class
window,factor-method	Sequence-class
window,GappedRanges-method	GappedRanges-class
window,GroupedIRanges-method	XVectorList-class
window,IRanges-method	IRanges-class
window,NULL-method	Sequence-class
window,Rle-method	Rle-class
window,Sequence-method	Sequence-class
window,vector-method	Sequence-class
window,XVector-method	XVector-class
window,XVectorList-method	XVectorList-class
window<-,DataTable-method	DataTable-class
window<-,factor-method	Sequence-class
window<-,RangedData-method	RangedData-class
window<-,Sequence-method	Sequence-class
window<-,vector-method	Sequence-class
with,Sequence-method	Sequence-class
within,RangedData-method	RangedData-class
XDouble	XVector-class
XDouble-class	XVector-class
XInteger	XVector-class
XInteger-class	XVector-class
XIntegerViews	XIntegerViews-class
XIntegerViews-class	XIntegerViews-class
XNumeric	XVector-class
XRaw	XVector-class
XRaw-class	XVector-class
XRawList	XVectorList-class
XRawList-class	XVectorList-class
xtabs,ANY,DataTable,ANY,missing-method	DataTable-stats
xtabs,ANY,DataTable-method	DataTable-stats
xvcopy	IRanges-internals
xvcopy,SharedRaw-method	IRanges-internals
xvcopy,SharedVector_Pool-method	IRanges-internals
xvcopy,XRawList-method	IRanges-internals
xvcopy,XVector-method	IRanges-internals
XVector	XVector-class
XVector-class	XVector-class
XVectorList	XVectorList-class
XVectorList-class	XVectorList-class
[,CompressedIRangesList-method	IRangesList-class
[,CompressedList-method	SimpleList-class
[,CompressedSplitDataFrameList-method	DataFrameList-class
[,DataFrame-method	DataFrame-class
[,FilterRules-method	FilterRules-class
[,GappedRanges-method	GappedRanges-class
[,GroupedIRanges-method	XVectorList-class
[,IRanges-method	IRanges-class
[,MaskCollection-method	MaskCollection-class
[,RangedData-method	RangedData-class
[,Ranges-method	Ranges-class
[,RangesList-method	RangesList-class
[,Rle-method	Rle-class
[,Sequence-method	Sequence-class
[,SimpleIRangesList-method	IRangesList-class
[,SimpleList-method	SimpleList-class
[,SimpleRangesList-method	RangesList-class
[,SimpleSplitDataFrameList-method	DataFrameList-class
[,XDouble-method	XVector-class
[,XInteger-method	XVector-class
[,XRaw-method	XVector-class
[,XVectorList-method	XVectorList-class
[<-,CompressedSplitDataFrameList-method	DataFrameList-class
[<-,DataFrame-method	DataFrame-class
[<-,IRanges-method	IRanges-class
[<-,RangedData-method	RangedData-class
[<-,Rle-method	Rle-class
[<-,Sequence-method	Sequence-class
[<-,SimpleSplitDataFrameList-method	DataFrameList-class
[<-,XVectorList-method	XVectorList-class
[[,Binning-method	Grouping-class
[[,CompressedList-method	SimpleList-class
[[,CompressedNormalIRangesList-method	IRangesList-class
[[,DataFrame-method	DataFrame-class
[[,GappedRanges-method	GappedRanges-class
[[,H2LGrouping-method	Grouping-class
[[,MaskCollection-method	MaskCollection-class
[[,Partitioning-method	Grouping-class
[[,RangedData-method	RangedData-class
[[,Ranges-method	Ranges-class
[[,Sequence-method	Sequence-class
[[,SharedRaw_Pool-method	IRanges-internals
[[,SimpleList-method	SimpleList-class
[[,Views-method	Views-class
[[,XVectorList-method	XVectorList-class
[[<-,CompressedList-method	SimpleList-class
[[<-,DataFrame-method	DataFrame-class
[[<-,FilterRules-method	FilterRules-class
[[<-,RangedData-method	RangedData-class
[[<-,SimpleList-method	SimpleList-class
[[<-,XVectorList-method	XVectorList-class
