$,GenomicRanges-method	GRanges-class
$,SummarizedExperiment-method	SummarizedExperiment-class
$<-,GenomicRanges-method	GRanges-class
$<-,SummarizedExperiment,ANY-method	SummarizedExperiment-class
$<-,SummarizedExperiment-method	SummarizedExperiment-class
%in%,ANY,GappedAlignments-method	findOverlaps-methods
%in%,GappedAlignmentPairs,ANY-method	findOverlaps-methods
%in%,GappedAlignments,ANY-method	findOverlaps-methods
%in%,GappedAlignments,GappedAlignments-method	findOverlaps-methods
%in%,GenomicRanges,GenomicRanges-method	findOverlaps-methods
%in%,GenomicRanges,GRangesList-method	findOverlaps-methods
%in%,GenomicRanges,RangedData-method	findOverlaps-methods
%in%,GenomicRanges,RangesList-method	findOverlaps-methods
%in%,GRangesList,GenomicRanges-method	findOverlaps-methods
%in%,GRangesList,GRangesList-method	findOverlaps-methods
%in%,GRangesList,RangedData-method	findOverlaps-methods
%in%,GRangesList,RangesList-method	findOverlaps-methods
%in%,RangedData,GenomicRanges-method	findOverlaps-methods
%in%,RangedData,GRangesList-method	findOverlaps-methods
%in%,RangesList,GenomicRanges-method	findOverlaps-methods
%in%,RangesList,GRangesList-method	findOverlaps-methods
<,GenomicRanges,GenomicRanges-method	GenomicRanges-comparison
<=,GenomicRanges,GenomicRanges-method	GenomicRanges-comparison
==,GenomicRanges,GenomicRanges-method	GenomicRanges-comparison
>,GenomicRanges,GenomicRanges-method	GenomicRanges-comparison
>=,GenomicRanges,GenomicRanges-method	GenomicRanges-comparison
as.data.frame,GappedAlignments-method	GappedAlignments-class
as.data.frame,GenomicRanges-method	GRanges-class
as.data.frame,GRangesList-method	GRangesList-class
as.data.frame,Seqinfo-method	Seqinfo-class
assay	SummarizedExperiment-class
assay,SummarizedExperiment,ANY-method	SummarizedExperiment-class
assay,SummarizedExperiment,character-method	SummarizedExperiment-class
assay,SummarizedExperiment,missing-method	SummarizedExperiment-class
assay,SummarizedExperiment,numeric-method	SummarizedExperiment-class
assay<-	SummarizedExperiment-class
assay<-,SummarizedExperiment,character,matrix-method	SummarizedExperiment-class
assay<-,SummarizedExperiment,missing,matrix-method	SummarizedExperiment-class
assay<-,SummarizedExperiment,numeric,matrix-method	SummarizedExperiment-class
assays	SummarizedExperiment-class
assays,SummarizedExperiment-method	SummarizedExperiment-class
Assays-class	SummarizedExperiment-class
assays<-	SummarizedExperiment-class
assays<-,SummarizedExperiment,list-method	SummarizedExperiment-class
assays<-,SummarizedExperiment,SimpleList-method	SummarizedExperiment-class
c,GappedAlignments-method	GappedAlignments-class
c,GenomicRanges-method	GRanges-class
checkConstraint	constraint
cigar	GappedAlignments-class
cigar,GappedAlignments-method	GappedAlignments-class
cigar-utils	cigar-utils
cigarNarrow	cigar-utils
cigarOpTable	cigar-utils
cigarQNarrow	cigar-utils
cigarToCigarTable	cigar-utils
cigarToIRanges	cigar-utils
cigarToIRangesListByAlignment	cigar-utils
cigarToIRangesListByRName	cigar-utils
cigarToQWidth	cigar-utils
cigarToRleList	cigar-utils
cigarToWidth	cigar-utils
class:Constraint	constraint
class:ConstraintORNULL	constraint
class:GappedAlignmentPairs	GappedAlignmentPairs-class
class:GappedAlignments	GappedAlignments-class
class:GenomicRanges	GRanges-class
class:GenomicRangesList	GenomicRangesList-class
class:GRanges	GRanges-class
class:GRangesList	GRangesList-class
class:Seqinfo	Seqinfo-class
class:SimpleGenomicRangesList	GenomicRangesList-class
coerce,GappedAlignmentPairs,GRangesList-method	GappedAlignmentPairs-class
coerce,GappedAlignments,GRanges-method	GappedAlignments-class
coerce,GappedAlignments,GRangesList-method	GappedAlignments-class
coerce,GappedAlignments,Ranges-method	GappedAlignments-class
coerce,GappedAlignments,RangesList-method	GappedAlignments-class
coerce,GenomicRanges,GappedAlignments-method	GRanges-class
coerce,GenomicRanges,RangedData-method	GRanges-class
coerce,GenomicRanges,RangesList-method	GRanges-class
coerce,GRangesList,CompressedIRangesList-method	GRangesList-class
coerce,GRangesList,IRangesList-method	GRangesList-class
coerce,RangedData,GRanges-method	GRanges-class
coerce,RangedDataList,GenomicRangesList-method	GenomicRangesList-class
coerce,RangedDataList,GRangesList-method	GRangesList-class
coerce,RangesList,GRanges-method	GRanges-class
coerce,RangesMapping,GenomicRanges-method	map-methods
coerce,RleList,GRanges-method	GRanges-class
coerce,RleViewsList,GRanges-method	GRanges-class
coerce,Seqinfo,GenomicRanges-method	Seqinfo-class
coerce,Seqinfo,GRanges-method	Seqinfo-class
coerce,Seqinfo,RangesList-method	Seqinfo-class
colData	SummarizedExperiment-class
colData,SummarizedExperiment-method	SummarizedExperiment-class
colData<-	SummarizedExperiment-class
colData<-,SummarizedExperiment,DataFrame-method	SummarizedExperiment-class
compare,ANY,SummarizedExperiment-method	SummarizedExperiment-class
compare,GenomicRanges,GenomicRanges-method	GenomicRanges-comparison
compare,SummarizedExperiment,ANY-method	SummarizedExperiment-class
compare,SummarizedExperiment,SummarizedExperiment-method	SummarizedExperiment-class
Constraint	constraint
constraint	constraint
Constraint-class	constraint
constraint<-	constraint
ConstraintORNULL	constraint
ConstraintORNULL-class	constraint
Constraints	constraint
countCompatibleOverlaps	encodeOverlaps-methods
countGenomicOverlaps	countGenomicOverlaps
countOverlaps,ANY,GappedAlignments-method	findOverlaps-methods
countOverlaps,ANY,SummarizedExperiment-method	SummarizedExperiment-class
countOverlaps,GappedAlignmentPairs,ANY-method	findOverlaps-methods
countOverlaps,GappedAlignments,ANY-method	findOverlaps-methods
countOverlaps,GappedAlignments,GappedAlignments-method	findOverlaps-methods
countOverlaps,GenomicRanges,GenomicRanges-method	findOverlaps-methods
countOverlaps,GenomicRanges,GRangesList-method	findOverlaps-methods
countOverlaps,GenomicRanges,RangedData-method	findOverlaps-methods
countOverlaps,GenomicRanges,RangesList-method	findOverlaps-methods
countOverlaps,GRangesList,GenomicRanges-method	findOverlaps-methods
countOverlaps,GRangesList,GRangesList-method	findOverlaps-methods
countOverlaps,GRangesList,RangedData-method	findOverlaps-methods
countOverlaps,GRangesList,RangesList-method	findOverlaps-methods
countOverlaps,RangedData,GenomicRanges-method	findOverlaps-methods
countOverlaps,RangedData,GRangesList-method	findOverlaps-methods
countOverlaps,RangesList,GenomicRanges-method	findOverlaps-methods
countOverlaps,RangesList,GRangesList-method	findOverlaps-methods
countOverlaps,SummarizedExperiment,ANY-method	SummarizedExperiment-class
countOverlaps,SummarizedExperiment,SummarizedExperiment-method	SummarizedExperiment-class
coverage,GappedAlignmentPairs-method	coverage-methods
coverage,GappedAlignments-method	coverage-methods
coverage,GenomicRanges-method	coverage-methods
coverage,GRangesList-method	coverage-methods
coverage,SummarizedExperiment-method	SummarizedExperiment-class
coverage-methods	coverage-methods
dim,SummarizedExperiment-method	SummarizedExperiment-class
dimnames,SummarizedExperiment-method	SummarizedExperiment-class
dimnames<-,SummarizedExperiment,list-method	SummarizedExperiment-class
dimnames<-,SummarizedExperiment,NULL-method	SummarizedExperiment-class
disjoin,GenomicRanges-method	inter-range-methods
disjoin,GRangesList-method	GRangesList-class
disjointBins,GenomicRanges-method	inter-range-methods
disjointBins,SummarizedExperiment-method	SummarizedExperiment-class
distance,ANY,SummarizedExperiment-method	SummarizedExperiment-class
distance,GenomicRanges,GenomicRanges-method	nearest-methods
distance,SummarizedExperiment,ANY-method	SummarizedExperiment-class
distance,SummarizedExperiment,SummarizedExperiment-method	SummarizedExperiment-class
distanceToNearest,ANY,SummarizedExperiment-method	SummarizedExperiment-class
distanceToNearest,GenomicRanges,GenomicRanges-method	nearest-methods
distanceToNearest,GenomicRanges,missing-method	nearest-methods
distanceToNearest,SummarizedExperiment,ANY-method	SummarizedExperiment-class
distanceToNearest,SummarizedExperiment,SummarizedExperiment-method	SummarizedExperiment-class
duplicated,GenomicRanges-method	GenomicRanges-comparison
duplicated,SummarizedExperiment-method	SummarizedExperiment-class
elementMetadata,GRangesList-method	GRangesList-class
elementMetadata,SummarizedExperiment-method	SummarizedExperiment-class
elementMetadata<-,GappedAlignmentPairs-method	GappedAlignmentPairs-class
elementMetadata<-,GappedAlignments-method	GappedAlignments-class
elementMetadata<-,GenomicRanges-method	GRanges-class
elementMetadata<-,GRangesList-method	GRangesList-class
elementMetadata<-,SummarizedExperiment-method	SummarizedExperiment-class
encodeOverlaps,GRangesList,GRangesList-method	encodeOverlaps-methods
encodeOverlaps-methods	encodeOverlaps-methods
end,GappedAlignments-method	GappedAlignments-class
end,GenomicRanges-method	GRanges-class
end,GRangesList-method	GRangesList-class
end,SummarizedExperiment-method	SummarizedExperiment-class
end<-,GenomicRanges-method	GRanges-class
end<-,GRangesList-method	GRangesList-class
end<-,SummarizedExperiment-method	SummarizedExperiment-class
exptData	SummarizedExperiment-class
exptData,SummarizedExperiment-method	SummarizedExperiment-class
exptData<-	SummarizedExperiment-class
exptData<-,SummarizedExperiment,list-method	SummarizedExperiment-class
exptData<-,SummarizedExperiment,SimpleList-method	SummarizedExperiment-class
extractQueryStartInTranscript	encodeOverlaps-methods
extractSkippedExonRanks	encodeOverlaps-methods
extractSkippedExonRanks,character-method	encodeOverlaps-methods
extractSkippedExonRanks,factor-method	encodeOverlaps-methods
extractSkippedExonRanks,OverlapEncodings-method	encodeOverlaps-methods
extractSpannedExonRanks	encodeOverlaps-methods
extractSpannedExonRanks,character-method	encodeOverlaps-methods
extractSpannedExonRanks,factor-method	encodeOverlaps-methods
extractSpannedExonRanks,OverlapEncodings-method	encodeOverlaps-methods
extractSteppedExonRanks	encodeOverlaps-methods
extractSteppedExonRanks,character-method	encodeOverlaps-methods
extractSteppedExonRanks,factor-method	encodeOverlaps-methods
extractSteppedExonRanks,OverlapEncodings-method	encodeOverlaps-methods
findCompatibleOverlaps	encodeOverlaps-methods
findCompatibleOverlaps,GappedAlignmentPairs,GRangesList-method	encodeOverlaps-methods
findCompatibleOverlaps,GappedAlignments,GRangesList-method	encodeOverlaps-methods
findOverlaps,ANY,GappedAlignments-method	findOverlaps-methods
findOverlaps,ANY,SummarizedExperiment-method	SummarizedExperiment-class
findOverlaps,GappedAlignmentPairs,ANY-method	findOverlaps-methods
findOverlaps,GappedAlignments,ANY-method	findOverlaps-methods
findOverlaps,GappedAlignments,GappedAlignments-method	findOverlaps-methods
findOverlaps,GenomicRanges,GenomicRanges-method	findOverlaps-methods
findOverlaps,GenomicRanges,GRangesList-method	findOverlaps-methods
findOverlaps,GenomicRanges,RangedData-method	findOverlaps-methods
findOverlaps,GenomicRanges,RangesList-method	findOverlaps-methods
findOverlaps,GRangesList,GenomicRanges-method	findOverlaps-methods
findOverlaps,GRangesList,GRangesList-method	findOverlaps-methods
findOverlaps,GRangesList,RangedData-method	findOverlaps-methods
findOverlaps,GRangesList,RangesList-method	findOverlaps-methods
findOverlaps,RangedData,GenomicRanges-method	findOverlaps-methods
findOverlaps,RangedData,GRangesList-method	findOverlaps-methods
findOverlaps,RangesList,GenomicRanges-method	findOverlaps-methods
findOverlaps,RangesList,GRangesList-method	findOverlaps-methods
findOverlaps,SummarizedExperiment,ANY-method	SummarizedExperiment-class
findOverlaps,SummarizedExperiment,SummarizedExperiment-method	SummarizedExperiment-class
findOverlaps-methods	findOverlaps-methods
findSpliceOverlaps	findSpliceOverlaps-methods
findSpliceOverlaps,GappedAlignmentPairs,GRangesList-method	findSpliceOverlaps-methods
findSpliceOverlaps,GappedAlignments,GRangesList-method	findSpliceOverlaps-methods
findSpliceOverlaps,GRangesList,GRangesList-method	findSpliceOverlaps-methods
findSpliceOverlaps-methods	findSpliceOverlaps-methods
first	GappedAlignmentPairs-class
first,GappedAlignmentPairs-method	GappedAlignmentPairs-class
flank,GenomicRanges-method	intra-range-methods
flank,GRangesList-method	GRangesList-class
flank,SummarizedExperiment-method	SummarizedExperiment-class
flipQuery	encodeOverlaps-methods
follow,ANY,SummarizedExperiment-method	SummarizedExperiment-class
follow,GenomicRanges,GenomicRanges-method	nearest-methods
follow,GenomicRanges,missing-method	nearest-methods
follow,SummarizedExperiment,ANY-method	SummarizedExperiment-class
follow,SummarizedExperiment,SummarizedExperiment-method	SummarizedExperiment-class
GappedAlignmentPairs	GappedAlignmentPairs-class
GappedAlignmentPairs-class	GappedAlignmentPairs-class
GappedAlignments	GappedAlignments-class
GappedAlignments-class	GappedAlignments-class
gaps,GenomicRanges-method	inter-range-methods
genome	seqinfo
genome,ANY-method	seqinfo
genome,Seqinfo-method	Seqinfo-class
genome<-	seqinfo
genome<-,ANY-method	seqinfo
genome<-,Seqinfo-method	Seqinfo-class
GenomicRanges	GRanges-class
GenomicRanges-class	GRanges-class
GenomicRanges-comparison	GenomicRanges-comparison
GenomicRangesList	GenomicRangesList-class
GenomicRangesList-class	GenomicRangesList-class
GenomicRangesORGRangesList-class	GRanges-class
GenomicRangesORmissing-class	GRanges-class
GRanges	GRanges-class
granges	GappedAlignments-class
granges,GappedAlignments-method	GappedAlignments-class
granges,RangesMapping-method	map-methods
granges,SummarizedExperiment-method	SummarizedExperiment-class
GRanges-class	GRanges-class
GRangesList	GRangesList-class
GRangesList-class	GRangesList-class
grg	GappedAlignments-class
grglist	GappedAlignments-class
grglist,GappedAlignmentPairs-method	GappedAlignmentPairs-class
grglist,GappedAlignments-method	GappedAlignments-class
inter-range-methods	inter-range-methods
intersect,GRanges,GRanges-method	setops-methods
intersect,Seqinfo,Seqinfo-method	Seqinfo-class
IntersectionNotEmpty	summarizeOverlaps
IntersectionStrict	summarizeOverlaps
intra-range-methods	intra-range-methods
introns	GappedAlignments-class
introns,GappedAlignmentPairs-method	GappedAlignmentPairs-class
introns,GappedAlignments-method	GappedAlignments-class
isCircular	seqinfo
isCircular,ANY-method	seqinfo
isCircular,Seqinfo-method	Seqinfo-class
isCircular<-	seqinfo
isCircular<-,ANY-method	seqinfo
isCircular<-,Seqinfo-method	Seqinfo-class
isCompatibleWithSkippedExons	encodeOverlaps-methods
isCompatibleWithSkippedExons,character-method	encodeOverlaps-methods
isCompatibleWithSkippedExons,factor-method	encodeOverlaps-methods
isCompatibleWithSkippedExons,OverlapEncodings-method	encodeOverlaps-methods
isCompatibleWithSplicing	encodeOverlaps-methods
isCompatibleWithSplicing,character-method	encodeOverlaps-methods
isCompatibleWithSplicing,factor-method	encodeOverlaps-methods
isCompatibleWithSplicing,OverlapEncodings-method	encodeOverlaps-methods
isDisjoint,GenomicRanges-method	inter-range-methods
isDisjoint,GRangesList-method	GRangesList-class
isDisjoint,SummarizedExperiment-method	SummarizedExperiment-class
isProperPair	GappedAlignmentPairs-class
isProperPair,GappedAlignmentPairs-method	GappedAlignmentPairs-class
keepSeqlevels	seqlevels-utils
keepSeqlevels,GappedAlignments,character-method	seqlevels-utils
keepSeqlevels,GappedAlignments,GappedAlignments-method	seqlevels-utils
keepSeqlevels,GappedAlignments,GenomicRanges-method	seqlevels-utils
keepSeqlevels,GappedAlignments,GRangesList-method	seqlevels-utils
keepSeqlevels,GenomicRanges,character-method	seqlevels-utils
keepSeqlevels,GenomicRanges,GappedAlignments-method	seqlevels-utils
keepSeqlevels,GenomicRanges,GenomicRanges-method	seqlevels-utils
keepSeqlevels,GenomicRanges,GRangesList-method	seqlevels-utils
keepSeqlevels,GRangesList,character-method	seqlevels-utils
keepSeqlevels,GRangesList,GappedAlignments-method	seqlevels-utils
keepSeqlevels,GRangesList,GenomicRanges-method	seqlevels-utils
keepSeqlevels,GRangesList,GRangesList-method	seqlevels-utils
last	GappedAlignmentPairs-class
last,GappedAlignmentPairs-method	GappedAlignmentPairs-class
left	GappedAlignmentPairs-class
left,GappedAlignmentPairs-method	GappedAlignmentPairs-class
length,GappedAlignmentPairs-method	GappedAlignmentPairs-class
length,GappedAlignments-method	GappedAlignments-class
length,GenomicRanges-method	GRanges-class
length,Seqinfo-method	Seqinfo-class
makeGRangesListFromFeatureFragments	GRangesList-class
map,GenomicRanges,GappedAlignments-method	map-methods
map,GenomicRanges,GRangesList-method	map-methods
match,ANY,GappedAlignments-method	findOverlaps-methods
match,ANY,SummarizedExperiment-method	SummarizedExperiment-class
match,GappedAlignmentPairs,ANY-method	findOverlaps-methods
match,GappedAlignments,ANY-method	findOverlaps-methods
match,GappedAlignments,GappedAlignments-method	findOverlaps-methods
match,GenomicRanges,GenomicRanges-method	findOverlaps-methods
match,GenomicRanges,GRangesList-method	findOverlaps-methods
match,GenomicRanges,RangedData-method	findOverlaps-methods
match,GenomicRanges,RangesList-method	findOverlaps-methods
match,GRangesList,GenomicRanges-method	findOverlaps-methods
match,GRangesList,GRangesList-method	findOverlaps-methods
match,GRangesList,RangedData-method	findOverlaps-methods
match,GRangesList,RangesList-method	findOverlaps-methods
match,RangedData,GenomicRanges-method	findOverlaps-methods
match,RangedData,GRangesList-method	findOverlaps-methods
match,RangesList,GenomicRanges-method	findOverlaps-methods
match,RangesList,GRangesList-method	findOverlaps-methods
match,SummarizedExperiment,ANY-method	SummarizedExperiment-class
match,SummarizedExperiment,SummarizedExperiment-method	SummarizedExperiment-class
mcols,SummarizedExperiment-method	SummarizedExperiment-class
mcols<-,SummarizedExperiment-method	SummarizedExperiment-class
merge,missing,Seqinfo-method	Seqinfo-class
merge,NULL,Seqinfo-method	Seqinfo-class
merge,Seqinfo,missing-method	Seqinfo-class
merge,Seqinfo,NULL-method	Seqinfo-class
merge,Seqinfo,Seqinfo-method	Seqinfo-class
names,GappedAlignmentPairs-method	GappedAlignmentPairs-class
names,GappedAlignments-method	GappedAlignments-class
names,GenomicRanges-method	GRanges-class
names,Seqinfo-method	Seqinfo-class
names<-,GappedAlignmentPairs-method	GappedAlignmentPairs-class
names<-,GappedAlignments-method	GappedAlignments-class
names<-,GenomicRanges-method	GRanges-class
names<-,Seqinfo-method	Seqinfo-class
narrow,GappedAlignments-method	GappedAlignments-class
narrow,GenomicRanges-method	intra-range-methods
narrow,SummarizedExperiment-method	SummarizedExperiment-class
nearest,ANY,SummarizedExperiment-method	SummarizedExperiment-class
nearest,GenomicRanges,GenomicRanges-method	nearest-methods
nearest,GenomicRanges,missing-method	nearest-methods
nearest,SummarizedExperiment,ANY-method	SummarizedExperiment-class
nearest,SummarizedExperiment,missing-method	SummarizedExperiment-class
nearest,SummarizedExperiment,SummarizedExperiment-method	SummarizedExperiment-class
nearest-methods	nearest-methods
ngap,GappedAlignmentPairs-method	GappedAlignmentPairs-class
ngap,GappedAlignments-method	GappedAlignments-class
Ops,GenomicRanges,numeric-method	intra-range-methods
order,GenomicRanges-method	GenomicRanges-comparison
order,SummarizedExperiment-method	SummarizedExperiment-class
pgap,GRanges,GRanges-method	setops-methods
phicoef	phicoef
pintersect,GappedAlignments,GRanges-method	setops-methods
pintersect,GRanges,GappedAlignments-method	setops-methods
pintersect,GRanges,GRanges-method	setops-methods
pintersect,GRanges,GRangesList-method	setops-methods
pintersect,GRangesList,GRanges-method	setops-methods
pintersect,GRangesList,GRangesList-method	setops-methods
precede,ANY,SummarizedExperiment-method	SummarizedExperiment-class
precede,GenomicRanges,GenomicRanges-method	nearest-methods
precede,GenomicRanges,missing-method	nearest-methods
precede,SummarizedExperiment,ANY-method	SummarizedExperiment-class
precede,SummarizedExperiment,SummarizedExperiment-method	SummarizedExperiment-class
psetdiff,GRanges,GRanges-method	setops-methods
psetdiff,GRanges,GRangesList-method	setops-methods
psetdiff,GRangesList,GRangesList-method	setops-methods
punion,GRanges,GRanges-method	setops-methods
punion,GRanges,GRangesList-method	setops-methods
punion,GRangesList,GRanges-method	setops-methods
qnarrow	GappedAlignments-class
qnarrow,GappedAlignments-method	GappedAlignments-class
queryLoc2refLoc	cigar-utils
queryLocs2refLocs	cigar-utils
qwidth	GappedAlignments-class
qwidth,GappedAlignments-method	GappedAlignments-class
range,GenomicRanges-method	inter-range-methods
range,GRangesList-method	GRangesList-class
ranges,GappedAlignments-method	GappedAlignments-class
ranges,GRanges-method	GRanges-class
ranges,GRangesList-method	GRangesList-class
ranges,SummarizedExperiment-method	SummarizedExperiment-class
ranges<-,GenomicRanges-method	GRanges-class
ranges<-,GRangesList-method	GRangesList-class
ranges<-,SummarizedExperiment-method	SummarizedExperiment-class
rank,GenomicRanges-method	GenomicRanges-comparison
rank,SummarizedExperiment-method	SummarizedExperiment-class
readGappedAlignmentPairs	GappedAlignmentPairs-class
readGappedAlignments	GappedAlignments-class
reduce,GenomicRanges-method	inter-range-methods
reduce,GRangesList-method	GRangesList-class
renameSeqlevels	seqlevels-utils
renameSeqlevels,GappedAlignments,character-method	seqlevels-utils
renameSeqlevels,GenomicRanges,character-method	seqlevels-utils
renameSeqlevels,GRangesList,character-method	seqlevels-utils
resize,GenomicRanges-method	intra-range-methods
resize,SummarizedExperiment-method	SummarizedExperiment-class
restrict,GenomicRanges-method	intra-range-methods
restrict,GRangesList-method	GRangesList-class
restrict,SummarizedExperiment-method	SummarizedExperiment-class
rglist	GappedAlignments-class
rglist,GappedAlignments-method	GappedAlignments-class
right	GappedAlignmentPairs-class
right,GappedAlignmentPairs-method	GappedAlignmentPairs-class
rname	GappedAlignments-class
rname,GappedAlignments-method	GappedAlignments-class
rname<-	GappedAlignments-class
rname<-,GappedAlignments-method	GappedAlignments-class
rowData	SummarizedExperiment-class
rowData,SummarizedExperiment-method	SummarizedExperiment-class
rowData<-	SummarizedExperiment-class
rowData<-,SummarizedExperiment,GenomicRanges-method	SummarizedExperiment-class
rowData<-,SummarizedExperiment,GRangesList-method	SummarizedExperiment-class
score,GenomicRanges-method	GRanges-class
score,GRangesList-method	GRangesList-class
selectEncodingWithCompatibleStrand	encodeOverlaps-methods
Seqinfo	Seqinfo-class
seqinfo	seqinfo
seqinfo,GappedAlignmentPairs-method	GappedAlignmentPairs-class
seqinfo,GappedAlignments-method	GappedAlignments-class
seqinfo,GRanges-method	GRanges-class
seqinfo,GRangesList-method	GRangesList-class
seqinfo,List-method	seqinfo
seqinfo,RangedData-method	seqinfo
seqinfo,RangesList-method	seqinfo
seqinfo,SummarizedExperiment-method	SummarizedExperiment-class
Seqinfo-class	Seqinfo-class
seqinfo<-	seqinfo
seqinfo<-,GappedAlignmentPairs-method	GappedAlignmentPairs-class
seqinfo<-,GappedAlignments-method	GappedAlignments-class
seqinfo<-,GenomicRanges-method	GRanges-class
seqinfo<-,GRangesList-method	GRangesList-class
seqinfo<-,List-method	seqinfo
seqinfo<-,RangedData-method	seqinfo
seqinfo<-,SummarizedExperiment-method	SummarizedExperiment-class
seqlengths	seqinfo
seqlengths,ANY-method	seqinfo
seqlengths,Seqinfo-method	Seqinfo-class
seqlengths<-	seqinfo
seqlengths<-,ANY-method	seqinfo
seqlengths<-,Seqinfo-method	Seqinfo-class
seqlevels	seqinfo
seqlevels,ANY-method	seqinfo
seqlevels,Seqinfo-method	Seqinfo-class
seqlevels<-	seqinfo
seqlevels<-,ANY-method	seqinfo
seqlevels<-,Seqinfo-method	Seqinfo-class
seqnames	seqinfo
seqnames,GappedAlignmentPairs-method	GappedAlignmentPairs-class
seqnames,GappedAlignments-method	GappedAlignments-class
seqnames,GRanges-method	GRanges-class
seqnames,GRangesList-method	GRangesList-class
seqnames,RangedData-method	seqinfo
seqnames,RangesList-method	seqinfo
seqnames,Seqinfo-method	Seqinfo-class
seqnames,SummarizedExperiment-method	SummarizedExperiment-class
seqnames<-	seqinfo
seqnames<-,GappedAlignments-method	GappedAlignments-class
seqnames<-,GenomicRanges-method	GRanges-class
seqnames<-,GRangesList-method	GRangesList-class
seqnames<-,Seqinfo-method	Seqinfo-class
seqnameStyle	seqinfo
seqnameStyle,ANY-method	seqinfo
seqnameStyle,Seqinfo-method	Seqinfo-class
seqnameStyle<-	seqinfo
seqnameStyle<-,ANY-method	seqinfo
seqselect,GenomicRanges-method	GRanges-class
seqselect<-,GenomicRanges-method	GRanges-class
setdiff,GRanges,GRanges-method	setops-methods
setops-methods	setops-methods
shift,GenomicRanges-method	intra-range-methods
shift,GRangesList-method	GRangesList-class
shift,SummarizedExperiment-method	SummarizedExperiment-class
show,GappedAlignmentPairs-method	GappedAlignmentPairs-class
show,GappedAlignments-method	GappedAlignments-class
show,GenomicRanges-method	GRanges-class
show,GRangesList-method	GRangesList-class
show,Seqinfo-method	Seqinfo-class
show,SummarizedExperiment-method	SummarizedExperiment-class
SimpleGenomicRangesList-class	GenomicRangesList-class
sort,GenomicRanges-method	GenomicRanges-comparison
sort,SummarizedExperiment-method	SummarizedExperiment-class
splitCigar	cigar-utils
start,GappedAlignments-method	GappedAlignments-class
start,GenomicRanges-method	GRanges-class
start,GRangesList-method	GRangesList-class
start,SummarizedExperiment-method	SummarizedExperiment-class
start<-,GenomicRanges-method	GRanges-class
start<-,GRangesList-method	GRangesList-class
start<-,SummarizedExperiment-method	SummarizedExperiment-class
strand,character-method	strand-utils
strand,DataTable-method	strand-utils
strand,factor-method	strand-utils
strand,GappedAlignmentPairs-method	GappedAlignmentPairs-class
strand,GappedAlignments-method	GappedAlignments-class
strand,GRanges-method	GRanges-class
strand,GRangesList-method	GRangesList-class
strand,integer-method	strand-utils
strand,logical-method	strand-utils
strand,missing-method	strand-utils
strand,Rle-method	strand-utils
strand,SummarizedExperiment-method	SummarizedExperiment-class
strand-utils	strand-utils
strand<-,DataTable-method	strand-utils
strand<-,GappedAlignments-method	GappedAlignments-class
strand<-,GenomicRanges-method	GRanges-class
strand<-,GRangesList-method	GRangesList-class
strand<-,SummarizedExperiment-method	SummarizedExperiment-class
subsetByOverlaps,ANY,GappedAlignments-method	findOverlaps-methods
subsetByOverlaps,GappedAlignmentPairs,ANY-method	findOverlaps-methods
subsetByOverlaps,GappedAlignments,ANY-method	findOverlaps-methods
subsetByOverlaps,GappedAlignments,GappedAlignments-method	findOverlaps-methods
subsetByOverlaps,GenomicRanges,GenomicRanges-method	findOverlaps-methods
subsetByOverlaps,GenomicRanges,GRangesList-method	findOverlaps-methods
subsetByOverlaps,GenomicRanges,RangedData-method	findOverlaps-methods
subsetByOverlaps,GenomicRanges,RangesList-method	findOverlaps-methods
subsetByOverlaps,GRangesList,GenomicRanges-method	findOverlaps-methods
subsetByOverlaps,GRangesList,GRangesList-method	findOverlaps-methods
subsetByOverlaps,GRangesList,RangedData-method	findOverlaps-methods
subsetByOverlaps,GRangesList,RangesList-method	findOverlaps-methods
subsetByOverlaps,RangedData,GenomicRanges-method	findOverlaps-methods
subsetByOverlaps,RangedData,GRangesList-method	findOverlaps-methods
subsetByOverlaps,RangesList,GenomicRanges-method	findOverlaps-methods
subsetByOverlaps,RangesList,GRangesList-method	findOverlaps-methods
summarizeCigarTable	cigar-utils
SummarizedExperiment	SummarizedExperiment-class
SummarizedExperiment,list-method	SummarizedExperiment-class
SummarizedExperiment,matrix-method	SummarizedExperiment-class
SummarizedExperiment,missing-method	SummarizedExperiment-class
SummarizedExperiment,SimpleList-method	SummarizedExperiment-class
SummarizedExperiment-class	SummarizedExperiment-class
summarizeOverlaps	summarizeOverlaps
summarizeOverlaps,GRanges,GappedAlignmentPairs-method	summarizeOverlaps
summarizeOverlaps,GRanges,GappedAlignments-method	summarizeOverlaps
summarizeOverlaps,GRangesList,GappedAlignmentPairs-method	summarizeOverlaps
summarizeOverlaps,GRangesList,GappedAlignments-method	summarizeOverlaps
Union	summarizeOverlaps
union,GRanges,GRanges-method	setops-methods
unique,GenomicRanges-method	GenomicRanges-comparison
unlist,GappedAlignmentPairs-method	GappedAlignmentPairs-class
updateObject,GappedAlignments-method	GappedAlignments-class
updateObject,GRanges-method	GRanges-class
updateObject,GRangesList-method	GRangesList-class
updateObject,Seqinfo-method	Seqinfo-class
updateObject,SummarizedExperiment-method	SummarizedExperiment-class
validCigar	cigar-utils
values,SummarizedExperiment-method	SummarizedExperiment-class
values<-,SummarizedExperiment-method	SummarizedExperiment-class
width,GappedAlignments-method	GappedAlignments-class
width,GenomicRanges-method	GRanges-class
width,GRangesList-method	GRangesList-class
width,SummarizedExperiment-method	SummarizedExperiment-class
width<-,GenomicRanges-method	GRanges-class
width<-,GRangesList-method	GRangesList-class
width<-,SummarizedExperiment-method	SummarizedExperiment-class
window,GenomicRanges-method	GRanges-class
[,GappedAlignmentPairs-method	GappedAlignmentPairs-class
[,GappedAlignments-method	GappedAlignments-class
[,GenomicRanges-method	GRanges-class
[,GRangesList-method	GRangesList-class
[,Seqinfo-method	Seqinfo-class
[,SummarizedExperiment-method	SummarizedExperiment-class
[<-,GenomicRanges,ANY,ANY,ANY-method	GRanges-class
[<-,GRangesList,ANY,ANY,ANY-method	GRangesList-class
[<-,SummarizedExperiment,ANY,ANY,SummarizedExperiment-method	SummarizedExperiment-class
[[,GappedAlignmentPairs,ANY,ANY-method	GappedAlignmentPairs-class
[[,SummarizedExperiment,ANY,missing-method	SummarizedExperiment-class
[[<-,GRangesList,ANY,ANY-method	GRangesList-class
[[<-,GRangesList-method	GRangesList-class
[[<-,SummarizedExperiment,ANY,missing,ANY-method	SummarizedExperiment-class
[[<-,SummarizedExperiment,ANY,missing-method	SummarizedExperiment-class
