!,CompressedList-method	CompressedList-class
$<-,CompressedList-method	CompressedList-class
$<-,RangedData-method	RangedData-class
%outside%	findOverlaps-methods
%over%	findOverlaps-methods
%within%	findOverlaps-methods
acbind	bind-arrays
acbind,array-method	bind-arrays
active	MaskCollection-class
active,MaskCollection-method	MaskCollection-class
active<-	MaskCollection-class
active<-,MaskCollection-method	MaskCollection-class
all,CompressedAtomicList-method	AtomicList-utils
all,CompressedRleList-method	AtomicList-utils
any,CompressedAtomicList-method	AtomicList-utils
anyNA,CompressedAtomicList-method	AtomicList-utils
append,MaskCollection,MaskCollection-method	MaskCollection-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
arbind	bind-arrays
arbind,array-method	bind-arrays
as.data.frame,GappedRanges-method	GappedRanges-class
as.data.frame,Hits-method	Hits-class-leftovers
as.data.frame,RangedData-method	RangedData-class
as.data.frame,Ranges-method	Ranges-class
as.env,RangedData-method	RangedData-class
as.env,SDFLWrapperForTransform-method	DataFrameList-class
as.integer,Ranges-method	Ranges-class
as.list,CompressedAtomicList-method	AtomicList-class
as.list,CompressedNormalIRangesList-method	IRangesList-class
as.list,Hits-method	Hits-class-leftovers
as.list,SortedByQueryHits-method	Hits-class-leftovers
as.matrix,AtomicList-method	AtomicList-class
as.matrix,CompressedHitsList-method	CompressedHitsList-class
as.matrix,Ranges-method	Ranges-class
as.matrix,Views-method	Views-class
as.matrix,ViewsList-method	ViewsList-class
as.vector,AtomicList-method	AtomicList-class
asNormalIRanges	IRanges-utils
AtomicList	AtomicList-class
AtomicList-class	AtomicList-class
AtomicList-utils	AtomicList-utils
bind arrays	bind-arrays
bind-arrays	bind-arrays
breakInChunks	IRanges-utils
c,CompressedList-method	CompressedList-class
c,GappedRanges-method	GappedRanges-class
c,IRanges-method	IRanges-class
c,RangedData-method	RangedData-class
c,Views-method	Views-class
cbind,DataFrameList-method	DataFrameList-class
CharacterList	AtomicList-class
CharacterList-class	AtomicList-class
chartr,ANY,ANY,CompressedCharacterList-method	AtomicList-utils
chartr,ANY,ANY,CompressedRleList-method	AtomicList-utils
chartr,ANY,ANY,SimpleCharacterList-method	AtomicList-utils
chartr,ANY,ANY,SimpleRleList-method	AtomicList-utils
class:AtomicList	AtomicList-class
class:CharacterList	AtomicList-class
class:ComplexList	AtomicList-class
class:CompressedAtomicList	AtomicList-class
class:CompressedCharacterList	AtomicList-class
class:CompressedComplexList	AtomicList-class
class:CompressedFactorList	AtomicList-class
class:CompressedGrouping	Grouping-class
class:CompressedHitsList	CompressedHitsList-class
class:CompressedIntegerList	AtomicList-class
class:CompressedIRangesList	IRangesList-class
class:CompressedList	CompressedList-class
class:CompressedLogicalList	AtomicList-class
class:CompressedManyToManyGrouping	Grouping-class
class:CompressedManyToOneGrouping	Grouping-class
class:CompressedNormalIRangesList	IRangesList-class
class:CompressedNumericList	AtomicList-class
class:CompressedRawList	AtomicList-class
class:CompressedRleList	AtomicList-class
class:Dups	Grouping-class
class:FactorList	AtomicList-class
class:functionORNULL	IRanges-internals
class:GappedRanges	GappedRanges-class
class:Grouping	Grouping-class
class:GroupingIRanges	Grouping-class
class:GroupingRanges	Grouping-class
class:H2LGrouping	Grouping-class
class:IntegerList	AtomicList-class
class:IRanges	IRanges-class
class:IRangesList	IRangesList-class
class:LogicalList	AtomicList-class
class:ManyToManyGrouping	Grouping-class
class:ManyToOneGrouping	Grouping-class
class:MaskCollection	MaskCollection-class
class:NCList	NCList-class
class:NCLists	NCList-class
class:NormalIRanges	IRanges-class
class:NormalIRangesList	IRangesList-class
class:NumericList	AtomicList-class
class:Partitioning	Grouping-class
class:PartitioningByEnd	Grouping-class
class:PartitioningByWidth	Grouping-class
class:PartitioningMap	Grouping-class
class:RangedData	RangedData-class
class:Ranges	Ranges-class
class:RangesList-class	RangesList-class
class:RangesORmissing	nearest-methods
class:RawList	AtomicList-class
class:RleList	AtomicList-class
class:RleViews	RleViews-class
class:SimpleAtomicList	AtomicList-class
class:SimpleCharacterList	AtomicList-class
class:SimpleComplexList	AtomicList-class
class:SimpleFactorList	AtomicList-class
class:SimpleGrouping	Grouping-class
class:SimpleIntegerList	AtomicList-class
class:SimpleIRangesList	IRangesList-class
class:SimpleLogicalList	AtomicList-class
class:SimpleManyToManyGrouping	Grouping-class
class:SimpleManyToOneGrouping	Grouping-class
class:SimpleNormalIRangesList	IRangesList-class
class:SimpleNumericList	AtomicList-class
class:SimpleRangesList-class	RangesList-class
class:SimpleRawList	AtomicList-class
class:SimpleRleList	AtomicList-class
class:SimpleViewsList	ViewsList-class
class:Views	Views-class
class:ViewsList	ViewsList-class
classNameForDisplay,CompressedList-method	CompressedList-class
coerce,ANY,CompressedList-method	CompressedList-class
coerce,ANY,CompressedSplitDataFrameList-method	DataFrameList-class
coerce,ANY,SimpleSplitDataFrameList-method	DataFrameList-class
coerce,ANY,SplitDataFrameList-method	DataFrameList-class
coerce,ANY,vector-method	IRanges-internals
coerce,AtomicList,CharacterList-method	AtomicList-class
coerce,AtomicList,ComplexList-method	AtomicList-class
coerce,AtomicList,IntegerList-method	AtomicList-class
coerce,AtomicList,LogicalList-method	AtomicList-class
coerce,AtomicList,NumericList-method	AtomicList-class
coerce,AtomicList,RawList-method	AtomicList-class
coerce,AtomicList,RleList-method	AtomicList-class
coerce,AtomicList,RleViews	AtomicList-class
coerce,CompressedAtomicList,list-method	AtomicList-class
coerce,CompressedIRangesList,CompressedNormalIRangesList-method	RangesList-class
coerce,CompressedIRangesList,GappedRanges-method	GappedRanges-class
coerce,CompressedNormalIRangesList,GappedRanges-method	GappedRanges-class
coerce,CompressedRleList,CompressedIRangesList-method	AtomicList-class
coerce,data.frame,RangedData-method	RangedData-class
coerce,DataFrame,Grouping-method	Grouping-class
coerce,DataFrame,SplitDataFrameList-method	DataFrameList-class
coerce,DataFrameList,DataFrame-method	DataFrameList-class
coerce,DataTable,RangedData-method	RangedData-class
coerce,FactorList,Grouping-method	Grouping-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,grouping,Grouping-method	Grouping-class
coerce,grouping,ManyToOneGrouping-method	Grouping-class
coerce,Hits,CompressedIntegerList-method	Hits-class-leftovers
coerce,Hits,DataFrame-method	Hits-class-leftovers
coerce,Hits,Grouping	Hits-class-leftovers
coerce,Hits,Grouping-method	Grouping-class
coerce,Hits,IntegerList-method	Hits-class-leftovers
coerce,Hits,List-method	Hits-class-leftovers
coerce,integer,IRanges-method	IRanges-class
coerce,integer,NormalIRanges-method	IRanges-class
coerce,IRanges,NormalIRanges-method	IRanges-utils
coerce,List,CompressedSplitDataFrameList-method	DataFrameList-class
coerce,list,RangesList-method	RangesList-class
coerce,List,SimpleSplitDataFrameList-method	DataFrameList-class
coerce,list,SplitDataFrameList-method	DataFrameList-class
coerce,logical,IRanges-method	IRanges-class
coerce,logical,NormalIRanges-method	IRanges-class
coerce,LogicalList,CompressedIRangesList-method	RangesList-class
coerce,LogicalList,CompressedNormalIRangesList-method	RangesList-class
coerce,LogicalList,IRangesList-method	RangesList-class
coerce,LogicalList,NormalIRangesList-method	RangesList-class
coerce,LogicalList,SimpleIRangesList-method	RangesList-class
coerce,LogicalList,SimpleNormalIRangesList-method	RangesList-class
coerce,ManyToOneGrouping,factor-method	Grouping-class
coerce,MaskCollection,NormalIRanges-method	MaskCollection-class
coerce,NCList,IRanges-method	NCList-class
coerce,NCLists,CompressedIRangesList-method	NCList-class
coerce,NCLists,IRangesList-method	NCList-class
coerce,NormalIRangesList,CompressedNormalIRangesList-method	RangesList-class
coerce,numeric,IRanges-method	IRanges-class
coerce,numeric,NormalIRanges-method	IRanges-class
coerce,RangedData,CompressedIRangesList-method	RangedData-class
coerce,RangedData,DataFrame-method	RangedData-class
coerce,RangedData,IRangesList-method	RangedData-class
coerce,RangedData,RangesList-method	RangedData-class
coerce,Ranges,IRanges-method	IRanges-class
coerce,Ranges,NCList-method	NCList-class
coerce,Ranges,PartitioningByEnd-method	Grouping-class
coerce,Ranges,PartitioningByWidth-method	Grouping-class
coerce,Ranges,RangedData-method	RangedData-class
coerce,Ranges,RangesList-method	RangesList-class
coerce,RangesList,CompressedIRangesList-method	RangesList-class
coerce,RangesList,CompressedNormalIRangesList-method	RangesList-class
coerce,RangesList,IRangesList-method	RangesList-class
coerce,RangesList,NCLists-method	NCList-class
coerce,RangesList,NormalIRangesList-method	RangesList-class
coerce,RangesList,RangedData-method	RangedData-class
coerce,RangesList,RangedSelection-method	RangedSelection-class
coerce,RangesList,SimpleIRangesList-method	RangesList-class
coerce,RangesList,SimpleNormalIRangesList-method	RangesList-class
coerce,RangesList,SimpleRangesList-method	RangesList-class
coerce,Rle,IRanges-method	Rle-class-leftovers
coerce,Rle,NormalIRanges-method	Rle-class-leftovers
coerce,Rle,RangedData-method	RangedData-class
coerce,RleList,CompressedIRangesList-method	RangesList-class
coerce,RleList,CompressedNormalIRangesList-method	RangesList-class
coerce,RleList,IRangesList-method	RangesList-class
coerce,RleList,NormalIRangesList-method	RangesList-class
coerce,RleList,RangedData-method	RangedData-class
coerce,RleList,SimpleIRangesList-method	RangesList-class
coerce,RleList,SimpleNormalIRangesList-method	RangesList-class
coerce,RleViewsList,CompressedIRangesList-method	RleViewsList-class
coerce,RleViewsList,IRangesList-method	RleViewsList-class
coerce,RleViewsList,RangedData-method	RangedData-class
coerce,RleViewsList,SimpleIRangesList-method	RleViewsList-class
coerce,SimpleIRangesList,SimpleNormalIRangesList-method	RangesList-class
coerce,SimpleList,SplitDataFrameList-method	DataFrameList-class
coerce,SimpleRangesList,SimpleIRangesList-method	RangesList-class
coerce,SortedByQueryHits,CompressedIntegerList-method	Hits-class-leftovers
coerce,SortedByQueryHits,IntegerList-method	Hits-class-leftovers
coerce,SortedByQueryHits,IRanges-method	Hits-class-leftovers
coerce,SortedByQueryHits,List-method	Hits-class-leftovers
coerce,SortedByQueryHits,Partitioning-method	Hits-class-leftovers
coerce,SortedByQueryHits,PartitioningByEnd-method	Hits-class-leftovers
coerce,SortedByQueryHits,Ranges-method	Hits-class-leftovers
coerce,SplitDataFrameList,DataFrame-method	DataFrameList-class
coerce,vector,AtomicList-method	AtomicList-class
coerce,vector,CompressedCharacterList-method	AtomicList-class
coerce,vector,CompressedComplexList-method	AtomicList-class
coerce,vector,CompressedIntegerList-method	AtomicList-class
coerce,vector,CompressedLogicalList-method	AtomicList-class
coerce,vector,CompressedNumericList-method	AtomicList-class
coerce,vector,CompressedRawList-method	AtomicList-class
coerce,vector,CompressedRleList-method	AtomicList-class
coerce,vector,Grouping-method	Grouping-class
coerce,vector,ManyToManyGrouping-method	Grouping-class
coerce,vector,ManyToOneGrouping-method	Grouping-class
coerce,vector,SimpleCharacterList-method	AtomicList-class
coerce,vector,SimpleComplexList-method	AtomicList-class
coerce,vector,SimpleIntegerList-method	AtomicList-class
coerce,vector,SimpleLogicalList-method	AtomicList-class
coerce,vector,SimpleNumericList-method	AtomicList-class
coerce,vector,SimpleRawList-method	AtomicList-class
coerce,vector,SimpleRleList-method	AtomicList-class
coerce,Vector,Views-method	Views-class
coerce,Views,IRanges-method	Views-class
coerce,Views,NormalIRanges-method	Views-class
coerce,Views,Ranges-method	Views-class
collapse	MaskCollection-class
collapse,MaskCollection-method	MaskCollection-class
colnames,CompressedSplitDataFrameList-method	DataFrameList-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<-,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
Complex,CompressedAtomicList-method	AtomicList-utils
Complex,SimpleAtomicList-method	AtomicList-utils
ComplexList	AtomicList-class
ComplexList-class	AtomicList-class
CompressedAtomicList	AtomicList-class
CompressedAtomicList-class	AtomicList-class
CompressedCharacterList	AtomicList-class
CompressedCharacterList-class	AtomicList-class
CompressedComplexList	AtomicList-class
CompressedComplexList-class	AtomicList-class
CompressedFactorList	AtomicList-class
CompressedFactorList-class	AtomicList-class
CompressedGrouping-class	Grouping-class
CompressedHitsList	CompressedHitsList-class
CompressedHitsList-class	CompressedHitsList-class
CompressedIntegerList	AtomicList-class
CompressedIntegerList-class	AtomicList-class
CompressedIRangesList	IRangesList-class
CompressedIRangesList-class	IRangesList-class
CompressedList	CompressedList-class
CompressedList-class	CompressedList-class
CompressedLogicalList	AtomicList-class
CompressedLogicalList-class	AtomicList-class
CompressedManyToManyGrouping-class	Grouping-class
CompressedManyToOneGrouping-class	Grouping-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,AtomicList,AtomicList-method	AtomicList-utils
countOverlaps	findOverlaps-methods
countOverlaps,RangedData,RangedData-method	findOverlaps-methods
countOverlaps,RangedData,RangesList-method	findOverlaps-methods
countOverlaps,Ranges,Ranges-method	findOverlaps-methods
countOverlaps,RangesList,RangedData-method	findOverlaps-methods
countOverlaps,RangesList,RangesList-method	findOverlaps-methods
countOverlaps,Vector,missing-method	findOverlaps-methods
countOverlaps,Vector,Vector-method	findOverlaps-methods
countOverlaps,Vector,ViewsList-method	findOverlaps-methods
countOverlaps,ViewsList,Vector-method	findOverlaps-methods
countOverlaps,ViewsList,ViewsList-method	findOverlaps-methods
cov,AtomicList,AtomicList-method	AtomicList-utils
coverage	coverage-methods
coverage,RangedData-method	coverage-methods
coverage,Ranges-method	coverage-methods
coverage,RangesList-method	coverage-methods
coverage,Views-method	coverage-methods
coverage-methods	coverage-methods
cummax,CompressedAtomicList-method	AtomicList-utils
cummin,CompressedAtomicList-method	AtomicList-utils
cumprod,CompressedAtomicList-method	AtomicList-utils
cumsum,CompressedAtomicList-method	AtomicList-utils
DataFrame-utils	DataFrame-utils
DataFrameList	DataFrameList-class
DataFrameList-class	DataFrameList-class
desc	MaskCollection-class
desc,MaskCollection-method	MaskCollection-class
desc<-	MaskCollection-class
desc<-,MaskCollection-method	MaskCollection-class
diff,CompressedIntegerList-method	AtomicList-utils
diff,CompressedNumericList-method	AtomicList-utils
diff,CompressedRleList-method	AtomicList-utils
diff,IntegerList-method	AtomicList-utils
diff,NumericList-method	AtomicList-utils
diff,RleList-method	AtomicList-utils
dim,DataFrameList-method	DataFrameList-class
dimnames,DataFrameList-method	DataFrameList-class
dimnames<-,DataFrameList-method	DataFrameList-class
disjoin	inter-range-methods
disjoin,CompressedIRangesList-method	inter-range-methods
disjoin,NormalIRanges-method	inter-range-methods
disjoin,Ranges-method	inter-range-methods
disjoin,RangesList-method	inter-range-methods
disjointBins	inter-range-methods
disjointBins,NormalIRanges-method	inter-range-methods
disjointBins,Ranges-method	inter-range-methods
disjointBins,RangesList-method	inter-range-methods
distance	nearest-methods
distance,Pairs,missing-method	nearest-methods
distance,Ranges,Ranges-method	nearest-methods
distanceToNearest	nearest-methods
distanceToNearest,Ranges,RangesORmissing-method	nearest-methods
drop,AtomicList-method	AtomicList-class
duplicated,CompressedAtomicList-method	AtomicList-class
duplicated,CompressedList-method	AtomicList-class
duplicated,Dups-method	Grouping-class
Dups	Grouping-class
Dups-class	Grouping-class
elementNROWS,CompressedList-method	CompressedList-class
elementNROWS,GappedRanges-method	GappedRanges-class
elementNROWS,NCLists-method	NCList-class
elementNROWS,RangedData-method	RangedData-class
elementNROWS,Ranges-method	Ranges-class
elementNROWS,Views-method	Views-class
end,CompressedIRangesList-method	IRangesList-class
end,GappedRanges-method	GappedRanges-class
end,NCList-method	NCList-class
end,NCLists-method	NCList-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,SimpleViewsList-method	ViewsList-class
end,Views-method	Views-class
end<-	Ranges-class
end<-,IRanges-method	IRanges-class
end<-,RangedData-method	RangedData-class
end<-,RangesList-method	RangesList-class
end<-,Views-method	Views-class
endoapply,CompressedList-method	CompressedList-class
endoapply,RangedData-method	RangedData-class
eval	Vector-class-leftovers
eval,expression,Vector-method	Vector-class-leftovers
eval,language,Vector-method	Vector-class-leftovers
extractList	extractList
extractList,ANY,ANY-method	extractList
extractList,ANY-method	extractList
FactorList	AtomicList-class
FactorList-class	AtomicList-class
filterRules,RDApplyParams-method	RDApplyParams-class
filterRules<-	RDApplyParams-class
filterRules<-,RDApplyParams-method	RDApplyParams-class
findOverlapPairs	findOverlaps-methods
findOverlaps	findOverlaps-methods
findOverlaps,ANY,Pairs-method	findOverlaps-methods
findOverlaps,integer,Ranges-method	findOverlaps-methods
findOverlaps,Pairs,ANY-method	findOverlaps-methods
findOverlaps,Pairs,missing-method	findOverlaps-methods
findOverlaps,Pairs,Pairs-method	findOverlaps-methods
findOverlaps,RangedData,RangedData-method	findOverlaps-methods
findOverlaps,RangedData,RangesList-method	findOverlaps-methods
findOverlaps,Ranges,Ranges-method	findOverlaps-methods
findOverlaps,RangesList,RangedData-method	findOverlaps-methods
findOverlaps,RangesList,RangesList-method	findOverlaps-methods
findOverlaps,Vector,missing-method	findOverlaps-methods
findOverlaps,Vector,Views-method	findOverlaps-methods
findOverlaps,Vector,ViewsList-method	findOverlaps-methods
findOverlaps,Views,Vector-method	findOverlaps-methods
findOverlaps,Views,Views-method	findOverlaps-methods
findOverlaps,ViewsList,Vector-method	findOverlaps-methods
findOverlaps,ViewsList,ViewsList-method	findOverlaps-methods
findOverlaps-methods	findOverlaps-methods
findRange	Rle-class-leftovers
findRange,Rle-method	Rle-class-leftovers
flank	intra-range-methods
flank,CompressedIRangesList-method	intra-range-methods
flank,Ranges-method	intra-range-methods
flank,RangesList-method	intra-range-methods
follow	nearest-methods
follow,Ranges,RangesORmissing-method	nearest-methods
from,CompressedHitsList-method	CompressedHitsList-class
functionORNULL	IRanges-internals
functionORNULL-class	IRanges-internals
GappedRanges	GappedRanges-class
GappedRanges-class	GappedRanges-class
gaps	inter-range-methods
gaps,CompressedIRangesList-method	inter-range-methods
gaps,MaskCollection-method	inter-range-methods
gaps,Ranges-method	inter-range-methods
gaps,RangesList-method	inter-range-methods
gaps,Views-method	inter-range-methods
Grouping	Grouping-class
Grouping-class	Grouping-class
GroupingIRanges	Grouping-class
GroupingIRanges-class	Grouping-class
GroupingRanges	Grouping-class
GroupingRanges-class	Grouping-class
grouplength	Grouping-class
grouplengths	Grouping-class
grouplengths,CompressedGrouping-method	Grouping-class
grouplengths,Grouping-method	Grouping-class
grouplengths,GroupingRanges-method	Grouping-class
grouplengths,H2LGrouping-method	Grouping-class
grouprank	Grouping-class
grouprank,H2LGrouping-method	Grouping-class
gsub,ANY,ANY,CompressedCharacterList-method	AtomicList-utils
gsub,ANY,ANY,CompressedRleList-method	AtomicList-utils
gsub,ANY,ANY,SimpleCharacterList-method	AtomicList-utils
gsub,ANY,ANY,SimpleRleList-method	AtomicList-utils
H2LGrouping	Grouping-class
H2LGrouping-class	Grouping-class
high2low	Grouping-class
high2low,ANY-method	Grouping-class
high2low,H2LGrouping-method	Grouping-class
Hits-examples	Hits-class-leftovers
IntegerList	AtomicList-class
IntegerList-class	AtomicList-class
inter-range-methods	inter-range-methods
intersect	setops-methods
intersect,CompressedAtomicList,CompressedAtomicList-method	AtomicList-utils
intersect,CompressedIRangesList,CompressedIRangesList-method	setops-methods
intersect,Pairs,missing-method	setops-methods
intersect,Ranges,Ranges-method	setops-methods
intersect,RangesList,RangesList-method	setops-methods
intra-range-methods	intra-range-methods
IQR,AtomicList-method	AtomicList-utils
IRanges	IRanges-constructor
IRanges-class	IRanges-class
IRanges-constructor	IRanges-constructor
IRanges-utils	IRanges-utils
IRangesList	IRangesList-class
IRangesList-class	IRangesList-class
is.na,CompressedList-method	CompressedList-class
isDisjoint	inter-range-methods
isDisjoint,NormalIRanges-method	inter-range-methods
isDisjoint,Ranges-method	inter-range-methods
isDisjoint,RangesList-method	inter-range-methods
isEmpty,NormalIRanges-method	IRanges-class
isEmpty,Ranges-method	Ranges-class
isNormal	Ranges-class
isNormal,CompressedIRangesList-method	IRangesList-class
isNormal,IRanges-method	IRanges-class
isNormal,NormalIRanges-method	IRanges-class
isNormal,Ranges-method	Ranges-class
isNormal,RangesList-method	RangesList-class
isNormal,SimpleIRangesList-method	IRangesList-class
iteratorFun	RDApplyParams-class
iteratorFun,RDApplyParams-method	RDApplyParams-class
iteratorFun<-	RDApplyParams-class
iteratorFun<-,RDApplyParams-method	RDApplyParams-class
lapply,CompressedAtomicList-method	AtomicList-class
lapply,CompressedList-method	CompressedList-class
lapply,RangedData-method	RangedData-class
length,CompressedList-method	CompressedList-class
length,GappedRanges-method	GappedRanges-class
length,H2LGrouping-method	Grouping-class
length,MaskCollection-method	MaskCollection-class
length,NCList-method	NCList-class
length,NCLists-method	NCList-class
length,PartitioningByEnd-method	Grouping-class
length,RangedData-method	RangedData-class
length,Ranges-method	Ranges-class
length,Views-method	Views-class
length<-,H2LGrouping-method	Grouping-class
LogicalList	AtomicList-class
LogicalList-class	AtomicList-class
low2high	Grouping-class
low2high,H2LGrouping-method	Grouping-class
mad,AtomicList-method	AtomicList-utils
ManyToManyGrouping	Grouping-class
ManyToManyGrouping-class	Grouping-class
ManyToOneGrouping	Grouping-class
ManyToOneGrouping-class	Grouping-class
mapOrder	Grouping-class
mapOrder,PartitioningMap-method	Grouping-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,CompressedList,vector-method	CompressedList-class
match,Ranges,Ranges-method	Ranges-comparison
Math,CompressedAtomicList-method	AtomicList-utils
Math,SimpleAtomicList-method	AtomicList-utils
Math2,CompressedAtomicList-method	AtomicList-utils
Math2,SimpleAtomicList-method	AtomicList-utils
max,CompressedNormalIRangesList-method	IRangesList-class
max,MaskCollection-method	MaskCollection-class
max,NormalIRanges-method	IRanges-class
max,SimpleNormalIRangesList-method	IRangesList-class
max,Views-method	view-summarization-methods
mean,AtomicList-method	AtomicList-utils
mean,CompressedIntegerList-method	AtomicList-utils
mean,CompressedLogicalList-method	AtomicList-utils
mean,CompressedNumericList-method	AtomicList-utils
mean,CompressedRleList-method	AtomicList-utils
mean,Views-method	view-summarization-methods
median,AtomicList-method	AtomicList-utils
median,CompressedAtomicList-method	AtomicList-utils
members	Grouping-class
members,H2LGrouping-method	Grouping-class
members,ManyToOneGrouping-method	Grouping-class
mendoapply,CompressedList-method	CompressedList-class
merge,missing,RangesList-method	RangesList-class
merge,RangesList,missing-method	RangesList-class
merge,RangesList,RangesList-method	RangesList-class
mergeByOverlaps	findOverlaps-methods
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
min,Views-method	view-summarization-methods
mstack	Vector-class-leftovers
mstack,DataFrame-method	DataFrame-utils
mstack,Vector-method	Vector-class-leftovers
mstack,vector-method	Vector-class-leftovers
multisplit	multisplit
names,CompressedList-method	CompressedList-class
names,GappedRanges-method	GappedRanges-class
names,IRanges-method	IRanges-class
names,MaskCollection-method	MaskCollection-class
names,NCList-method	NCList-class
names,NCLists-method	NCList-class
names,Partitioning-method	Grouping-class
names,RangedData-method	RangedData-class
names,Views-method	Views-class
names<-,CompressedList-method	CompressedList-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<-,Views-method	Views-class
narrow	intra-range-methods
narrow,CompressedIRangesList-method	intra-range-methods
narrow,MaskCollection-method	intra-range-methods
narrow,Ranges-method	intra-range-methods
narrow,RangesList-method	intra-range-methods
narrow,Views-method	intra-range-methods
nchar,CompressedCharacterList-method	AtomicList-utils
nchar,CompressedRleList-method	AtomicList-utils
nchar,SimpleCharacterList-method	AtomicList-utils
nchar,SimpleRleList-method	AtomicList-utils
NCList	NCList-class
NCList-class	NCList-class
NCLists	NCList-class
NCLists-class	NCList-class
ncol,CompressedSplitDataFrameList-method	DataFrameList-class
ncol,DataFrameList-method	DataFrameList-class
ncol,RangedData-method	RangedData-class
ncol,SimpleSplitDataFrameList-method	DataFrameList-class
nearest	nearest-methods
nearest,Ranges,RangesORmissing-method	nearest-methods
nearest-methods	nearest-methods
ngap	GappedRanges-class
ngap,GappedRanges-method	GappedRanges-class
nir_list	MaskCollection-class
nir_list,MaskCollection-method	MaskCollection-class
nLnode,CompressedHitsList-method	CompressedHitsList-class
nobj	Grouping-class
nobj,BaseManyToManyGrouping-method	Grouping-class
nobj,CompressedManyToOneGrouping-method	Grouping-class
nobj,H2LGrouping-method	Grouping-class
nobj,ManyToManyGrouping-method	Grouping-class
nobj,ManyToOneGrouping-method	Grouping-class
nobj,PartitioningByEnd-method	Grouping-class
NormalIRanges	IRanges-class
NormalIRanges-class	IRanges-class
NormalIRangesList	IRangesList-class
NormalIRangesList-class	IRangesList-class
nRnode,CompressedHitsList-method	CompressedHitsList-class
nrow,DataFrameList-method	DataFrameList-class
nrow,RangedData-method	RangedData-class
NumericList	AtomicList-class
NumericList-class	AtomicList-class
Ops,atomic,AtomicList-method	AtomicList-utils
Ops,atomic,CompressedAtomicList-method	AtomicList-utils
Ops,atomic,SimpleAtomicList-method	AtomicList-utils
Ops,AtomicList,atomic-method	AtomicList-utils
Ops,CompressedAtomicList,atomic-method	AtomicList-utils
Ops,CompressedAtomicList,CompressedAtomicList-method	AtomicList-utils
Ops,CompressedAtomicList,SimpleAtomicList-method	AtomicList-utils
Ops,CompressedIRangesList,numeric-method	intra-range-methods
Ops,Ranges,ANY-method	intra-range-methods
Ops,Ranges,numeric-method	intra-range-methods
Ops,RangesList,numeric-method	intra-range-methods
Ops,SimpleAtomicList,atomic-method	AtomicList-utils
Ops,SimpleAtomicList,CompressedAtomicList-method	AtomicList-utils
Ops,SimpleAtomicList,SimpleAtomicList-method	AtomicList-utils
order,CompressedAtomicList-method	AtomicList-utils
order,List-method	AtomicList-class
order,Ranges-method	Ranges-comparison
overlapsAny	findOverlaps-methods
overlapsAny,RangedData,RangedData-method	findOverlaps-methods
overlapsAny,RangedData,RangesList-method	findOverlaps-methods
overlapsAny,RangesList,RangedData-method	findOverlaps-methods
overlapsAny,RangesList,RangesList-method	findOverlaps-methods
overlapsAny,Vector,missing-method	findOverlaps-methods
overlapsAny,Vector,Vector-method	findOverlaps-methods
overlapsAny,Vector,ViewsList-method	findOverlaps-methods
overlapsAny,ViewsList,Vector-method	findOverlaps-methods
overlapsAny,ViewsList,ViewsList-method	findOverlaps-methods
Partitioning	Grouping-class
Partitioning-class	Grouping-class
PartitioningByEnd	Grouping-class
PartitioningByEnd-class	Grouping-class
PartitioningByWidth	Grouping-class
PartitioningByWidth-class	Grouping-class
PartitioningMap	Grouping-class
PartitioningMap-class	Grouping-class
paste,CompressedAtomicList-method	AtomicList-utils
pcompare	Ranges-comparison
pcompare,Ranges,Ranges-method	Ranges-comparison
pgap	setops-methods
pgap,Ranges,Ranges-method	setops-methods
pintersect	setops-methods
pintersect,Pairs,missing-method	setops-methods
pintersect,Ranges,Ranges-method	setops-methods
pmax,IntegerList-method	AtomicList-utils
pmax,NumericList-method	AtomicList-utils
pmax,RleList-method	AtomicList-utils
pmax.int,IntegerList-method	AtomicList-utils
pmax.int,NumericList-method	AtomicList-utils
pmax.int,RleList-method	AtomicList-utils
pmin,IntegerList-method	AtomicList-utils
pmin,NumericList-method	AtomicList-utils
pmin,RleList-method	AtomicList-utils
pmin.int,IntegerList-method	AtomicList-utils
pmin.int,NumericList-method	AtomicList-utils
pmin.int,RleList-method	AtomicList-utils
poverlaps	findOverlaps-methods
poverlaps,integer,Ranges-method	findOverlaps-methods
poverlaps,Ranges,integer-method	findOverlaps-methods
poverlaps,Ranges,Ranges-method	findOverlaps-methods
precede	nearest-methods
precede,Ranges,RangesORmissing-method	nearest-methods
promoters	intra-range-methods
promoters,CompressedIRangesList-method	intra-range-methods
promoters,Ranges-method	intra-range-methods
promoters,RangesList-method	intra-range-methods
promoters,Views-method	intra-range-methods
psetdiff	setops-methods
psetdiff,Pairs,missing-method	setops-methods
psetdiff,Ranges,Ranges-method	setops-methods
punion	setops-methods
punion,Pairs,missing-method	setops-methods
punion,Ranges,Ranges-method	setops-methods
quantile,AtomicList-method	AtomicList-utils
range	inter-range-methods
range,CompressedIntegerList-method	AtomicList-utils
range,CompressedIRangesList-method	inter-range-methods
range,CompressedLogicalList-method	AtomicList-utils
range,CompressedNumericList-method	AtomicList-utils
range,RangedData-method	inter-range-methods
range,Ranges-method	inter-range-methods
range,RangesList-method	inter-range-methods
rangeComparisonCodeToLetter	Ranges-comparison
RangedData	RangedData-class
rangedData	RDApplyParams-class
rangedData,RDApplyParams-method	RDApplyParams-class
RangedData-class	RangedData-class
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	Views-class
ranges,CompressedRleList-method	AtomicList-class
ranges,Hits-method	findOverlaps-methods
ranges,HitsList-method	findOverlaps-methods
ranges,NCList-method	NCList-class
ranges,NCLists-method	NCList-class
ranges,RangedData-method	RangedData-class
ranges,RangedSelection-method	RangedSelection-class
ranges,Rle-method	Rle-class-leftovers
ranges,RleList-method	AtomicList-class
ranges,SimpleViewsList-method	ViewsList-class
ranges,Views-method	Views-class
Ranges-class	Ranges-class
Ranges-comparison	Ranges-comparison
ranges<-	Views-class
ranges<-,RangedData-method	RangedData-class
ranges<-,RangedSelection-method	RangedSelection-class
ranges<-,Views-method	Views-class
RangesList	RangesList-class
RangesList-class	RangesList-class
RangesORmissing	nearest-methods
RangesORmissing-class	nearest-methods
rank,CompressedAtomicList-method	AtomicList-utils
rank,List-method	AtomicList-class
RawList	AtomicList-class
RawList-class	AtomicList-class
rbind,DataFrameList-method	DataFrameList-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	inter-range-methods
reduce,CompressedIRangesList-method	inter-range-methods
reduce,RangedData-method	inter-range-methods
reduce,Ranges-method	inter-range-methods
reduce,RangesList-method	inter-range-methods
reduce,Views-method	inter-range-methods
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	intra-range-methods
reflect,Ranges-method	intra-range-methods
regroup	extractList
relist,ANY,List-method	extractList
relist,ANY,PartitioningByEnd-method	extractList
relist,Vector,list-method	extractList
relistToClass,data.frame-method	DataFrame-utils
relistToClass,DataFrame-method	DataFrame-utils
rep,Vector-method	Vector-class-leftovers
rep.int,Vector-method	Vector-class-leftovers
resize	intra-range-methods
resize,CompressedIRangesList-method	intra-range-methods
resize,IntervalList-method	intra-range-methods
resize,Ranges-method	intra-range-methods
resize,RangesList-method	intra-range-methods
restrict	intra-range-methods
restrict,CompressedIRangesList-method	intra-range-methods
restrict,Ranges-method	intra-range-methods
restrict,RangesList-method	intra-range-methods
rev,Vector-method	Vector-class-leftovers
revElements,CompressedList-method	CompressedList-class
reverse	reverse-methods
reverse,character-method	reverse-methods
reverse,IRanges-method	reverse-methods
reverse,MaskCollection-method	reverse-methods
reverse,NormalIRanges-method	reverse-methods
reverse,Views-method	reverse-methods
RleList	AtomicList-class
RleList,AtomicList,RleList-method	AtomicList-class
RleList-class	AtomicList-class
RleViews	RleViews-class
RleViews-class	RleViews-class
RleViewsList	RleViewsList-class
RleViewsList-class	RleViewsList-class
rownames,DataFrameList-method	DataFrameList-class
rownames,RangedData-method	RangedData-class
rownames<-,CompressedSplitDataFrameList-method	DataFrameList-class
rownames<-,RangedData-method	RangedData-class
rownames<-,SimpleDataFrameList-method	DataFrameList-class
runLength,CompressedRleList-method	AtomicList-class
runLength,RleList-method	AtomicList-class
runmean,RleList-method	AtomicList-utils
runmed,CompressedIntegerList-method	AtomicList-utils
runmed,NumericList-method	AtomicList-utils
runmed,RleList-method	AtomicList-utils
runmed,SimpleIntegerList-method	AtomicList-utils
runq,RleList-method	AtomicList-utils
runsum,RleList-method	AtomicList-utils
runValue,CompressedRleList-method	AtomicList-class
runValue,RleList-method	AtomicList-class
runValue<-,CompressedRleList-method	AtomicList-class
runValue<-,SimpleRleList-method	AtomicList-class
runwtsum,RleList-method	AtomicList-utils
score,RangedData-method	RangedData-class
score<-,RangedData-method	RangedData-class
sd,AtomicList-method	AtomicList-utils
selectNearest	nearest-methods
selfmatch,CompressedAtomicList-method	AtomicList-utils
selfmatch,Ranges-method	Ranges-comparison
setdiff	setops-methods
setdiff,CompressedIRangesList,CompressedIRangesList-method	setops-methods
setdiff,Pairs,missing-method	setops-methods
setdiff,Ranges,Ranges-method	setops-methods
setdiff,RangesList,RangesList-method	setops-methods
setops-methods	setops-methods
shift	intra-range-methods
shift,CompressedIRangesList-method	intra-range-methods
shift,Ranges-method	intra-range-methods
shift,RangesList-method	intra-range-methods
shift,Views-method	intra-range-methods
show,AtomicList-method	AtomicList-class
show,Dups-method	Grouping-class
show,GappedRanges-method	GappedRanges-class
show,Grouping-method	Grouping-class
show,MaskCollection-method	MaskCollection-class
show,PartitioningMap-method	Grouping-class
show,RangedData-method	RangedData-class
show,Ranges-method	Ranges-class
show,RangesList-method	RangesList-class
show,RleList-method	AtomicList-class
show,RleViews-method	RleViews-class
show,SplitDataFrameList-method	DataFrameList-class
showAsCell,Ranges-method	Ranges-class
showAsCell,RangesList-method	RangesList-class
SimpleAtomicList	AtomicList-class
SimpleAtomicList-class	AtomicList-class
SimpleCharacterList	AtomicList-class
SimpleCharacterList-class	AtomicList-class
SimpleComplexList	AtomicList-class
SimpleComplexList-class	AtomicList-class
SimpleDataFrameList-class	DataFrameList-class
SimpleFactorList	AtomicList-class
SimpleFactorList-class	AtomicList-class
SimpleGrouping-class	Grouping-class
SimpleIntegerList	AtomicList-class
SimpleIntegerList-class	AtomicList-class
SimpleIRangesList	IRangesList-class
SimpleIRangesList-class	IRangesList-class
SimpleLogicalList	AtomicList-class
SimpleLogicalList-class	AtomicList-class
SimpleManyToManyGrouping-class	Grouping-class
SimpleManyToOneGrouping-class	Grouping-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
SimpleViewsList	ViewsList-class
SimpleViewsList-class	ViewsList-class
simplify	RDApplyParams-class
simplify,RDApplyParams-method	RDApplyParams-class
simplify<-	RDApplyParams-class
simplify<-,RDApplyParams-method	RDApplyParams-class
slice	slice-methods
slice,ANY-method	slice-methods
slice,Rle-method	slice-methods
slice,RleList-method	slice-methods
slice-methods	slice-methods
slidingWindows	Ranges-class
slidingWindows,Ranges-method	Ranges-class
smoothEnds,CompressedIntegerList-method	AtomicList-utils
smoothEnds,NumericList-method	AtomicList-utils
smoothEnds,RleList-method	AtomicList-utils
smoothEnds,SimpleIntegerList-method	AtomicList-utils
solveUserSEW	IRanges-constructor
solveUserSEW0	IRanges-constructor
sort,List-method	AtomicList-class
space	RangesList-class
space,CompressedHitsList-method	CompressedHitsList-class
space,RangedData-method	RangedData-class
space,RangesList-method	RangesList-class
split,RangedData,ANY-method	RangedData-class
split<-,Vector-method	seqapply
splitAsList	extractList
splitAsList,ANY,ANY	extractList
SplitDataFrameList	DataFrameList-class
SplitDataFrameList-class	DataFrameList-class
splitRanges	Rle-class-leftovers
splitRanges,Rle-method	Rle-class-leftovers
splitRanges,vectorORfactor-method	Rle-class-leftovers
stack,DataFrameList-method	DataFrameList-class
stack,List-method	List-class-leftovers
stack,RangedDataList-method	RangedDataList-class
start,CompressedIRangesList-method	IRangesList-class
start,GappedRanges-method	GappedRanges-class
start,IRanges-method	IRanges-class
start,NCList-method	NCList-class
start,NCLists-method	NCList-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,SimpleViewsList-method	ViewsList-class
start,Views-method	Views-class
start<-	Ranges-class
start<-,IRanges-method	IRanges-class
start<-,RangedData-method	RangedData-class
start<-,RangesList-method	RangesList-class
start<-,Views-method	Views-class
sub,ANY,ANY,CompressedCharacterList-method	AtomicList-utils
sub,ANY,ANY,CompressedRleList-method	AtomicList-utils
sub,ANY,ANY,SimpleCharacterList-method	AtomicList-utils
sub,ANY,ANY,SimpleRleList-method	AtomicList-utils
subject	Views-class
subject,SimpleRleViewsList-method	RleViewsList-class
subject,Views-method	Views-class
subset,Vector-method	Vector-class-leftovers
subsetByOverlaps	findOverlaps-methods
subsetByOverlaps,RangedData,RangedData-method	findOverlaps-methods
subsetByOverlaps,RangedData,RangesList-method	findOverlaps-methods
subsetByOverlaps,RangesList,RangedData-method	findOverlaps-methods
subsetByOverlaps,Vector,Vector-method	findOverlaps-methods
subviews	Views-class
subviews,Views-method	Views-class
successiveIRanges	IRanges-utils
successiveViews	Views-class
sum,CompressedIntegerList-method	AtomicList-utils
sum,CompressedLogicalList-method	AtomicList-utils
sum,CompressedNumericList-method	AtomicList-utils
sum,Views-method	view-summarization-methods
Summary,AtomicList-method	AtomicList-utils
summary,CompressedIRangesList-method	IRangesList-class
Summary,CompressedRleList-method	AtomicList-utils
Summary,Views-method	view-summarization-methods
table,AtomicList-method	AtomicList-class
tapply,ANY,Vector-method	Vector-class-leftovers
tapply,Vector,ANY-method	Vector-class-leftovers
tapply,Vector,Vector-method	Vector-class-leftovers
threebands	intra-range-methods
threebands,IRanges-method	intra-range-methods
tile	Ranges-class
tile,Ranges-method	Ranges-class
to,CompressedHitsList-method	CompressedHitsList-class
togroup	Grouping-class
togroup,ANY-method	Grouping-class
togroup,H2LGrouping-method	Grouping-class
togroup,ManyToOneGrouping-method	Grouping-class
togroup,Partitioning-method	Grouping-class
togrouplength	Grouping-class
togrouplength,ManyToOneGrouping-method	Grouping-class
togrouprank	Grouping-class
togrouprank,H2LGrouping-method	Grouping-class
tolower,CompressedCharacterList-method	AtomicList-utils
tolower,CompressedRleList-method	AtomicList-utils
tolower,SimpleCharacterList-method	AtomicList-utils
tolower,SimpleRleList-method	AtomicList-utils
toupper,CompressedCharacterList-method	AtomicList-utils
toupper,CompressedRleList-method	AtomicList-utils
toupper,SimpleCharacterList-method	AtomicList-utils
toupper,SimpleRleList-method	AtomicList-utils
transform,SplitDataFrameList-method	DataFrameList-class
trim	Views-class
trim,Views-method	Views-class
union	setops-methods
union,CompressedIRangesList,CompressedIRangesList-method	setops-methods
union,Pairs,missing-method	setops-methods
union,Ranges,Ranges-method	setops-methods
union,RangesList,RangesList-method	setops-methods
unique,CompressedList-method	AtomicList-class
unique,RleList-method	AtomicList-class
universe	RangesList-class
universe,RangedData-method	RangedData-class
universe,RangesList-method	RangesList-class
universe,ViewsList-method	ViewsList-class
universe<-	RangesList-class
universe<-,RangedData-method	RangedData-class
universe<-,RangesList-method	RangesList-class
universe<-,ViewsList-method	ViewsList-class
unlist,CompressedList-method	CompressedList-class
unlist,IRangesList-method	IRangesList-class
unlist,RangedDataList-method	RangedDataList-class
unlist,Ranges-method	Ranges-class
unlist,SimpleFactorList-method	AtomicList-class
unlist,SimpleNormalIRangesList-method	IRangesList-class
unlist,SimpleRleList-method	AtomicList-class
unsplit,List-method	seqapply
unstrsplit,CharacterList-method	AtomicList-utils
unstrsplit,RleList-method	AtomicList-utils
update,IRanges-method	IRanges-class
update,Ranges-method	Ranges-class
values,RangedData-method	RangedData-class
values<-,RangedData-method	RangedData-class
var,AtomicList,AtomicList-method	AtomicList-utils
var,AtomicList,missing-method	AtomicList-utils
view-summarization-methods	view-summarization-methods
viewApply	view-summarization-methods
viewApply,RleViews-method	view-summarization-methods
viewApply,RleViewsList-method	view-summarization-methods
viewApply,Views-method	view-summarization-methods
viewMaxs	view-summarization-methods
viewMaxs,RleViews-method	view-summarization-methods
viewMaxs,RleViewsList-method	view-summarization-methods
viewMeans	view-summarization-methods
viewMeans,RleViews-method	view-summarization-methods
viewMeans,RleViewsList-method	view-summarization-methods
viewMins	view-summarization-methods
viewMins,RleViews-method	view-summarization-methods
viewMins,RleViewsList-method	view-summarization-methods
viewRangeMaxs	view-summarization-methods
viewRangeMaxs,RleViews-method	view-summarization-methods
viewRangeMaxs,RleViewsList-method	view-summarization-methods
viewRangeMins	view-summarization-methods
viewRangeMins,RleViews-method	view-summarization-methods
viewRangeMins,RleViewsList-method	view-summarization-methods
Views	Views-class
Views,Rle-method	RleViews-class
Views,RleList-method	RleViewsList-class
Views-class	Views-class
ViewsList	ViewsList-class
ViewsList-class	ViewsList-class
viewSums	view-summarization-methods
viewSums,RleViews-method	view-summarization-methods
viewSums,RleViewsList-method	view-summarization-methods
viewWhichMaxs	view-summarization-methods
viewWhichMaxs,RleViews-method	view-summarization-methods
viewWhichMaxs,RleViewsList-method	view-summarization-methods
viewWhichMins	view-summarization-methods
viewWhichMins,RleViews-method	view-summarization-methods
viewWhichMins,RleViewsList-method	view-summarization-methods
vmembers	Grouping-class
vmembers,H2LGrouping-method	Grouping-class
vmembers,ManyToOneGrouping-method	Grouping-class
which,CompressedLogicalList-method	AtomicList-utils
which,CompressedRleList-method	AtomicList-utils
which,SimpleLogicalList-method	AtomicList-utils
which,SimpleRleList-method	AtomicList-utils
which.max,CompressedRleList-method	AtomicList-utils
which.max,IntegerList-method	AtomicList-utils
which.max,NumericList-method	AtomicList-utils
which.max,RleList-method	AtomicList-utils
which.max,Views-method	view-summarization-methods
which.min,CompressedRleList-method	AtomicList-utils
which.min,IntegerList-method	AtomicList-utils
which.min,NumericList-method	AtomicList-utils
which.min,RleList-method	AtomicList-utils
which.min,Views-method	view-summarization-methods
whichAsIRanges	IRanges-utils
whichFirstNotNormal	Ranges-class
whichFirstNotNormal,Ranges-method	Ranges-class
whichFirstNotNormal,RangesList-method	RangesList-class
width	Ranges-class
width,CompressedIRangesList-method	IRangesList-class
width,IRanges-method	IRanges-class
width,MaskCollection-method	MaskCollection-class
width,NCList-method	NCList-class
width,NCLists-method	NCList-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,SimpleViewsList-method	ViewsList-class
width,Views-method	Views-class
width<-	Ranges-class
width<-,IRanges-method	IRanges-class
width<-,RangedData-method	RangedData-class
width<-,RangesList-method	RangesList-class
width<-,Views-method	Views-class
window<-,factor-method	Vector-class-leftovers
window<-,Vector-method	Vector-class-leftovers
window<-,vector-method	Vector-class-leftovers
window<-.factor	Vector-class-leftovers
window<-.Vector	Vector-class-leftovers
window<-.vector	Vector-class-leftovers
with,Vector-method	Vector-class-leftovers
within,RangedData-method	RangedData-class
[,CompressedSplitDataFrameList-method	DataFrameList-class
[,RangedData-method	RangedData-class
[,SimpleSplitDataFrameList-method	DataFrameList-class
[<-,SplitDataFrameList-method	DataFrameList-class
[[,RangedData-method	RangedData-class
[[,SDFLWrapperForTransform-method	DataFrameList-class
[[<-,CompressedList-method	CompressedList-class
[[<-,RangedData-method	RangedData-class
[[<-,SDFLWrapperForTransform-method	DataFrameList-class
