!=,integer,XIntegerViews-method	XIntegerViews-class
!=,integer,XRleIntegerViews-method	XRleIntegerViews-class
!=,Sequence,Sequence-method	Sequence-class
!=,SequencePtr,SequencePtr-method	IRanges-internals
!=,XInteger,XIntegerViews-method	XIntegerViews-class
!=,XIntegerViews,integer-method	XIntegerViews-class
!=,XIntegerViews,XInteger-method	XIntegerViews-class
!=,XIntegerViews,XIntegerViews-method	XIntegerViews-class
!=,XRleInteger,XRleIntegerViews-method	XRleIntegerViews-class
!=,XRleIntegerViews,integer-method	XRleIntegerViews-class
!=,XRleIntegerViews,XRleInteger-method	XRleIntegerViews-class
!=,XRleIntegerViews,XRleIntegerViews-method	XRleIntegerViews-class
$,ListLike-method	IRanges-internals
%in%,Ranges,Ranges-method	IntervalTree-class
==,integer,XIntegerViews-method	XIntegerViews-class
==,integer,XRleIntegerViews-method	XRleIntegerViews-class
==,SequencePtr,SequencePtr-method	IRanges-internals
==,XInteger,XInteger-method	Sequence-class
==,XInteger,XIntegerViews-method	XIntegerViews-class
==,XIntegerViews,integer-method	XIntegerViews-class
==,XIntegerViews,XInteger-method	XIntegerViews-class
==,XIntegerViews,XIntegerViews-method	XIntegerViews-class
==,XNumeric,XNumeric-method	Sequence-class
==,XRle,XRle-method	Sequence-class
==,XRleInteger,XRleIntegerViews-method	XRleIntegerViews-class
==,XRleIntegerViews,integer-method	XRleIntegerViews-class
==,XRleIntegerViews,XRleInteger-method	XRleIntegerViews-class
==,XRleIntegerViews,XRleIntegerViews-method	XRleIntegerViews-class
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
annotation	RangedData-class
annotation,RangedData-method	RangedData-class
append,FilterRules,FilterRules-method	FilterRules-class
append,MaskCollection,MaskCollection-method	MaskCollection-class
append,TypedList,TypedList-method	TypedList-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
Arith,integer,XRleInteger-method	Sequence-class
Arith,XRleInteger,integer-method	Sequence-class
Arith,XRleInteger,XRleInteger-method	Sequence-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,SplitXDataFrame-method	SplitXDataFrame-class
as.data.frame,XDataFrame-method	XDataFrame-class
as.integer,IntegerPtr-method	IRanges-internals
as.integer,RawPtr-method	IRanges-internals
as.integer,XInteger-method	Sequence-class
as.integer,XIntegerViews-method	XIntegerViews-class
as.integer,XRleInteger-method	Sequence-class
as.integer,XRleIntegerViews-method	XRleIntegerViews-class
as.list,ListLike-method	IRanges-internals
as.list,TypedList-method	TypedList-class
as.matrix,Ranges-method	Ranges-class
as.matrix,RangesMatching-method	RangesMatching-class
as.numeric,NumericPtr-method	IRanges-internals
as.numeric,XNumeric-method	Sequence-class
as.table,RangesMatching-method	RangesMatching-class
as.vector,XInteger,missing-method	Sequence-class
as.vector,XNumeric,missing-method	Sequence-class
as.vector,XRleInteger,missing-method	Sequence-class
asNormalIRanges	IRanges-utils
c,FilterRules-method	FilterRules-class
c,GenomicData-method	GenomicData-class
c,IRanges-method	IRanges-class
c,RangedData-method	RangedData-class
c,TypedList-method	TypedList-class
cbind	XDataFrame-class
cbind,XDataFrame-method	XDataFrame-class
characterORNULL	IRanges-internals
characterORNULL-class	IRanges-internals
chrom	GenomicData-class
chrom,GenomicData-method	GenomicData-class
class:characterORNULL	IRanges-internals
class:IntegerPtr	IRanges-internals
class:IRanges	IRanges-class
class:ListLike	IRanges-internals
class:MaskCollection	MaskCollection-class
class:NormalIRanges	IRanges-class
class:NumericPtr	IRanges-internals
class:Ranges	Ranges-class
class:RawPtr	IRanges-internals
class:Sequence	Sequence-class
class:SequenceORvector	Sequence-class
class:SequencePtr	IRanges-internals
class:Views	Views-class
class:XInteger	Sequence-class
class:XIntegerViews	XIntegerViews-class
class:XNumeric	Sequence-class
class:XRaw	Sequence-class
class:XRle	Sequence-class
class:XRleInteger	Sequence-class
class:XRleIntegerViews	XRleIntegerViews-class
class:XSequence	Sequence-class
coerce,ANY,XDataFrame-method	XDataFrame-class
coerce,data.frame,XDataFrame-method	XDataFrame-class
coerce,integer,XDataFrame-method	XDataFrame-class
coerce,integer,XInteger-method	Sequence-class
coerce,integer,XRleInteger-method	Sequence-class
coerce,integer,XSequence-method	Sequence-class
coerce,IntervalTree,IRanges-method	IntervalTree-class
coerce,IRanges,IntervalTree-method	IntervalTree-class
coerce,IRanges,NormalIRanges-method	IRanges-utils
coerce,IRangesList,NormalIRanges-method	IRangesList-class
coerce,MaskCollection,NormalIRanges-method	MaskCollection-class
coerce,matrix,XDataFrame-method	XDataFrame-class
coerce,numeric,XNumeric-method	Sequence-class
coerce,numeric,XSequence-method	Sequence-class
coerce,RangedData,XDataFrame-method	RangedData-class
coerce,Ranges,IntervalTree-method	IntervalTree-class
coerce,RangesList,IRangesList-method	RangesList-class
coerce,SplitXDataFrame,XDataFrame-method	SplitXDataFrame-class
coerce,TypedList,list-method	TypedList-class
coerce,Views,NormalIRanges-method	Views-class
coerce,XDataFrame,data.frame-method	XDataFrame-class
coerce,XRle,GenomicData-method	GenomicData-class
coerce,XRle,RangedData-method	RangedData-class
coverage	coverage
coverage,IRanges-method	coverage
coverage,MaskCollection-method	coverage
desc	MaskCollection-class
desc,MaskCollection-method	MaskCollection-class
desc<-	MaskCollection-class
desc<-,MaskCollection-method	MaskCollection-class
dim,RangedData-method	RangedData-class
dim,SplitXDataFrame-method	SplitXDataFrame-class
dim,XDataFrame-method	XDataFrame-class
dimnames,RangedData-method	RangedData-class
dimnames,SplitXDataFrame-method	SplitXDataFrame-class
dimnames,XDataFrame-method	XDataFrame-class
dimnames<-,XDataFrame,ANY-method	XDataFrame-class
duplicated,Ranges-method	Ranges-class
elementClass	TypedList-class
elementClass,TypedList-method	TypedList-class
elements	TypedList-class
elements,TypedList-method	TypedList-class
end,RangedData-method	RangedData-class
end,Ranges-method	Ranges-class
end,RangesList-method	RangesList-class
end,XRanges-method	XRanges-class
end<-	Ranges-class
end<-,IRanges-method	IRanges-class
eval,expressionORlanguage,RangedData-method	RangedData-utils
eval,expressionORlanguage,XDataFrame-method	XDataFrame-utils
eval,FilterRules,ANY-method	FilterRules-class
FilterRules	FilterRules-class
filterRules	RDApplyParams-class
filterRules,RDApplyParams-method	RDApplyParams-class
FilterRules-class	FilterRules-class
filterRules<-	RDApplyParams-class
filterRules<-,RDApplyParams-method	RDApplyParams-class
first	Ranges-class
first,Ranges-method	Ranges-class
gaps	IRanges-utils
gaps,IRanges-method	IRanges-utils
gaps,MaskCollection-method	MaskCollection-class
gaps,RangesList-method	RangesList-utils
gaps,Views-method	Views-class
gaps,XRanges-method	XRanges-class
genome	GenomicData-class
genome,GenomicData-method	GenomicData-class
GenomicData	GenomicData-class
GenomicData-class	GenomicData-class
IntegerPtr	IRanges-internals
IntegerPtr-class	IRanges-internals
intersect,IRanges,IRanges-method	IRanges-setops
IntervalTree	IntervalTree-class
IntervalTree-class	IntervalTree-class
intToAdjacentRanges	IRanges-utils
intToRanges	IRanges-utils
IRanges	IRanges-class
IRanges-class	IRanges-class
IRanges-setops	IRanges-setops
IRanges-utils	IRanges-utils
IRangesList	IRangesList-class
IRangesList-class	IRangesList-class
is.array,XDataFrame-method	XDataFrame-class
isEmpty	Ranges-class
isEmpty,MaskCollection-method	MaskCollection-class
isEmpty,NormalIRanges-method	IRanges-class
isEmpty,Ranges-method	Ranges-class
isEmpty,RangesList-method	RangesList-class
isNormal	Ranges-class
isNormal,Ranges-method	Ranges-class
isSingleInteger	IRanges-internals
isSingleIntegerOrNA	IRanges-internals
isSingleNumber	IRanges-internals
isSingleNumberOrNA	IRanges-internals
isSingleString	IRanges-internals
isSingleStringOrNA	IRanges-internals
isTRUEorFALSE	IRanges-internals
lapply,ListLike,ANY-method	IRanges-internals
lapply,TypedList,function-method	TypedList-class
last	Ranges-class
last,Ranges-method	Ranges-class
length,IntervalTree-method	IntervalTree-class
length,MaskCollection-method	MaskCollection-class
length,RangedData-method	RangedData-class
length,Ranges-method	Ranges-class
length,SequencePtr-method	IRanges-internals
length,TypedList-method	TypedList-class
length,XRle-method	Sequence-class
length,XSequence-method	Sequence-class
ListLike	IRanges-internals
ListLike-class	IRanges-internals
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
matchMatrix	RangesMatching-class
matchMatrix,RangesMatching-method	RangesMatching-class
max,MaskCollection-method	MaskCollection-class
max,NormalIRanges-method	IRanges-class
min,MaskCollection-method	MaskCollection-class
min,NormalIRanges-method	IRanges-class
names,IRanges-method	IRanges-class
names,MaskCollection-method	MaskCollection-class
names,RangedData-method	RangedData-class
names,TypedList-method	TypedList-class
names<-,IRanges-method	IRanges-class
names<-,MaskCollection-method	MaskCollection-class
names<-,RangedData-method	RangedData-class
names<-,TypedList-method	TypedList-class
narrow	IRanges-utils
narrow,IRanges-method	IRanges-utils
narrow,NormalIRanges-method	IRanges-utils
narrow,Views-method	Views-class
new2	IRanges-internals
newViews	Views-class
nir_list	MaskCollection-class
nir_list,MaskCollection-method	MaskCollection-class
NormalIRanges	IRanges-class
NormalIRanges-class	IRanges-class
NumericPtr	IRanges-internals
NumericPtr-class	IRanges-internals
overlap	IntervalTree-class
overlap,IntervalTree,Ranges-method	IntervalTree-class
overlap,Ranges,missing-method	IntervalTree-class
overlap,Ranges,Ranges-method	IntervalTree-class
pintersect	IRanges-setops
pintersect,IRanges,IRanges-method	IRanges-setops
psetdiff	IRanges-setops
psetdiff,IRanges,IRanges-method	IRanges-setops
punion	IRanges-setops
punion,IRanges,IRanges-method	IRanges-setops
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
Ranges	Ranges-class
ranges	RangedData-class
ranges,RangedData-method	RangedData-class
Ranges-class	Ranges-class
RangesList	RangesList-class
RangesList-class	RangesList-class
RangesList-utils	RangesList-utils
RangesMatching-class	RangesMatching-class
RawPtr	IRanges-internals
RawPtr-class	IRanges-internals
RawPtr.append	IRanges-internals
RawPtr.compare	IRanges-internals
RawPtr.copy	IRanges-internals
RawPtr.read	IRanges-internals
RawPtr.readComplexes	IRanges-internals
RawPtr.readInts	IRanges-internals
RawPtr.reverseCopy	IRanges-internals
RawPtr.write	IRanges-internals
RawPtr.writeInts	IRanges-internals
rbind	XDataFrame-class
rbind,XDataFrame-method	XDataFrame-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	IRanges-utils
reduce,IRanges-method	IRanges-utils
reduce,MaskCollection-method	MaskCollection-class
reduce,RangesList-method	RangesList-utils
reduce,XRanges-method	XRanges-class
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
rep,Ranges-method	Ranges-class
rep,Sequence-method	Sequence-class
rep,XRle-method	Sequence-class
restrict	IRanges-utils
restrict,IRanges-method	IRanges-utils
restrict,Views-method	Views-class
reverse	reverse
reverse,IRanges-method	reverse
reverse,MaskCollection-method	reverse
reverse,NormalIRanges-method	reverse
reverse,XRle-method	Sequence-class
safeExplode	IRanges-internals
sapply	IRanges-internals
sapply,ListLike-method	IRanges-internals
sapplyLength	IRanges-internals
Sequence	Sequence-class
Sequence-class	Sequence-class
SequenceORvector	Sequence-class
SequenceORvector-class	Sequence-class
SequencePtr	IRanges-internals
SequencePtr-class	IRanges-internals
setdiff,IRanges,IRanges-method	IRanges-setops
setValidity2	IRanges-internals
shift	IRanges-utils
shift,IRanges-method	IRanges-utils
show,externalptr-method	IRanges-internals
show,IntegerPtr-method	IRanges-internals
show,MaskCollection-method	MaskCollection-class
show,NumericPtr-method	IRanges-internals
show,RangedData-method	RangedData-class
show,Ranges-method	Ranges-class
show,RangesList-method	RangesList-class
show,RawPtr-method	IRanges-internals
show,TypedList-method	TypedList-class
show,XDataFrame-method	XDataFrame-class
show,XInteger-method	Sequence-class
show,XIntegerViews-method	XIntegerViews-class
show,XNumeric-method	Sequence-class
show,XRleInteger-method	Sequence-class
show,XRleIntegerViews-method	XRleIntegerViews-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,XInteger-method	Views-utils
slice,XRleInteger-method	Views-utils
solveUserSEW	solveUserSEW
split,RangedData-method	RangedData-class
split,Ranges-method	RangesList-class
split,XDataFrame-method	XDataFrame-class
SplitXDataFrame	SplitXDataFrame-class
SplitXDataFrame-class	SplitXDataFrame-class
start,IRanges-method	IRanges-class
start,RangedData-method	RangedData-class
start,Ranges-method	Ranges-class
start,RangesList-method	RangesList-class
start,XRanges-method	XRanges-class
start<-	Ranges-class
start<-,IRanges-method	IRanges-class
strand	GenomicData-class
strand,GenomicData-method	GenomicData-class
strand,missing-method	GenomicData-class
subject	Views-class
subject,Views-method	Views-class
subseq	Sequence-class
subseq,MaskCollection-method	MaskCollection-class
subseq,SequenceORvector-method	Sequence-class
subseq,XSequence-method	Sequence-class
subviews	Views-class
subviews,Views-method	Views-class
successiveIRanges	IRanges-utils
successiveViews	Views-class
summary,RangesList-method	RangesList-class
t,RangesMatching-method	RangesMatching-class
toNormalIRanges	IRanges-utils
toString,RawPtr-method	IRanges-internals
trim	Views-class
trim,Views-method	Views-class
TypedList-class	TypedList-class
union,IRanges,IRanges-method	IRanges-setops
unlist,IRangesList-method	IRangesList-class
unlist,SplitXDataFrame-method	SplitXDataFrame-class
unlist,TypedList-method	TypedList-class
update,IRanges-method	IRanges-class
values	RangedData-class
values,RangedData-method	RangedData-class
viewMaxs	Views-utils
viewMaxs,XIntegerViews-method	Views-utils
viewMaxs,XRleIntegerViews-method	Views-utils
viewMins	Views-utils
viewMins,XIntegerViews-method	Views-utils
viewMins,XRleIntegerViews-method	Views-utils
Views	Views-class
views	Views-class
Views,integer-method	XIntegerViews-class
Views,XInteger-method	XIntegerViews-class
Views,XRleInteger-method	XRleIntegerViews-class
Views-class	Views-class
Views-utils	Views-utils
viewSums	Views-utils
viewSums,XIntegerViews-method	Views-utils
viewSums,XRleIntegerViews-method	Views-utils
whichAsIRanges	IRanges-utils
whichFirstNotNormal	Ranges-class
whichFirstNotNormal,Ranges-method	Ranges-class
width	Ranges-class
width,IRanges-method	IRanges-class
width,MaskCollection-method	MaskCollection-class
width,RangedData-method	RangedData-class
width,Ranges-method	Ranges-class
width,RangesList-method	RangesList-class
width,XRanges-method	XRanges-class
width<-	Ranges-class
width<-,IRanges-method	IRanges-class
width<-,Views-method	Views-class
XDataFrame	XDataFrame-class
XDataFrame-class	XDataFrame-class
XDataFrame-utils	XDataFrame-utils
XInteger	Sequence-class
XInteger-class	Sequence-class
XIntegerViews	XIntegerViews-class
XIntegerViews-class	XIntegerViews-class
XNumeric	Sequence-class
XNumeric-class	Sequence-class
XRanges	XRanges-class
XRanges-class	XRanges-class
XRaw	Sequence-class
XRaw-class	Sequence-class
XRle	Sequence-class
XRle-class	Sequence-class
XRleInteger	Sequence-class
XRleInteger-class	Sequence-class
XRleIntegerViews	XRleIntegerViews-class
XRleIntegerViews-class	XRleIntegerViews-class
XSequence	Sequence-class
XSequence-class	Sequence-class
[,FilterRules,ANY,ANY,ANY-method	FilterRules-class
[,IRanges,ANY,ANY,ANY-method	IRanges-class
[,MaskCollection,ANY,ANY,ANY-method	MaskCollection-class
[,RangedData,ANY,ANY,ANY-method	RangedData-class
[,TypedList,ANY,ANY,ANY-method	TypedList-class
[,XDataFrame,ANY,ANY,ANY-method	XDataFrame-class
[,XInteger,ANY,ANY,ANY-method	Sequence-class
[,XNumeric,ANY,ANY,ANY-method	Sequence-class
[,XRle,ANY,ANY,ANY-method	Sequence-class
[<-,MaskCollection,ANY,ANY,ANY-method	MaskCollection-class
[<-,RangedData,ANY,ANY,ANY-method	RangedData-class
[<-,Ranges,ANY,ANY,ANY-method	Ranges-class
[<-,Sequence,ANY,ANY,ANY-method	Sequence-class
[<-,TypedList,ANY,ANY,ANY-method	TypedList-class
[[,ListLike-method	IRanges-internals
[[,MaskCollection-method	MaskCollection-class
[[,RangedData-method	RangedData-class
[[,TypedList-method	TypedList-class
[[,Views-method	Views-class
[[,XDataFrame-method	XDataFrame-class
[[,XIntegerViews-method	XIntegerViews-class
[[,XRleIntegerViews-method	XRleIntegerViews-class
[[<-,FilterRules-method	FilterRules-class
[[<-,MaskCollection-method	MaskCollection-class
[[<-,RangedData-method	RangedData-class
[[<-,TypedList-method	TypedList-class
[[<-,Views-method	Views-class
[[<-,XDataFrame-method	XDataFrame-class
[[<-,XIntegerViews-method	XIntegerViews-class
[[<-,XRleIntegerViews-method	XRleIntegerViews-class
