$,GenomicRanges-method	GRanges-class
$,SummarizedExperiment-method	SummarizedExperiment-class
$<-,GenomicRanges-method	GRanges-class
$<-,SummarizedExperiment,ANY-method	SummarizedExperiment-class
$<-,SummarizedExperiment-method	SummarizedExperiment-class
as.data.frame,GenomicRanges-method	GRanges-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,GenomicRanges-method	GRanges-class
cbind,SummarizedExperiment-method	SummarizedExperiment-class
checkConstraint	constraint
class:Constraint	constraint
class:ConstraintORNULL	constraint
class:GenomicRanges	GRanges-class
class:GenomicRangesList	GenomicRangesList-class
class:GIntervalTree	GIntervalTree-class
class:GRanges	GRanges-class
class:GRangesList	GRangesList-class
class:SimpleGenomicRangesList	GenomicRangesList-class
coerce,data.frame,GRanges-method	makeGRangesFromDataFrame
coerce,DataFrame,GRanges-method	makeGRangesFromDataFrame
coerce,GenomicRanges,RangedData-method	GRanges-class
coerce,GenomicRanges,RangesList-method	GRanges-class
coerce,GenomicRangesList,RangedDataList-method	GenomicRangesList-class
coerce,GIntervalTree,GRanges-method	GIntervalTree-class
coerce,GRanges,GIntervalTree-method	GIntervalTree-class
coerce,GRangesList,CompressedIRangesList-method	GRangesList-class
coerce,GRangesList,IRangesList-method	GRangesList-class
coerce,GRangesList,RangesList-method	GRangesList-class
coerce,GRangesMapping,GenomicRanges-method	GRangesMapping-class
coerce,GRangesMapping,RangedData-method	GRangesMapping-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,RleList,GRanges-method	GRanges-class
coerce,RleViewsList,GRanges-method	GRanges-class
coerce,Seqinfo,GenomicRanges-method	GRanges-class
coerce,Seqinfo,GRanges-method	GRanges-class
coerce,Seqinfo,RangesList-method	GRanges-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
countOverlaps	findOverlaps-methods
countOverlaps,GenomicRanges,GenomicRanges-method	findOverlaps-methods
countOverlaps,GenomicRanges,Vector-method	findOverlaps-methods
countOverlaps,GRanges,GRangesList-method	findOverlaps-methods
countOverlaps,GRangesList,GRanges-method	findOverlaps-methods
countOverlaps,GRangesList,GRangesList-method	findOverlaps-methods
countOverlaps,GRangesList,Vector-method	findOverlaps-methods
countOverlaps,SummarizedExperiment,SummarizedExperiment-method	SummarizedExperiment-class
countOverlaps,SummarizedExperiment,Vector-method	SummarizedExperiment-class
countOverlaps,Vector,GenomicRanges-method	findOverlaps-methods
countOverlaps,Vector,GRangesList-method	findOverlaps-methods
countOverlaps,Vector,SummarizedExperiment-method	SummarizedExperiment-class
coverage	coverage-methods
coverage,GenomicRanges-method	coverage-methods
coverage,GRangesList-method	coverage-methods
coverage,SummarizedExperiment-method	SummarizedExperiment-class
coverage-methods	coverage-methods
dim,GRangesMapping-method	GRangesMapping-class
dim,SummarizedExperiment-method	SummarizedExperiment-class
dimnames,SummarizedExperiment-method	SummarizedExperiment-class
dimnames<-,SummarizedExperiment,list-method	SummarizedExperiment-class
dimnames<-,SummarizedExperiment,NULL-method	SummarizedExperiment-class
disjoin	inter-range-methods
disjoin,GenomicRanges-method	inter-range-methods
disjoin,GRangesList-method	inter-range-methods
disjointBins	inter-range-methods
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
duplicated.GenomicRanges	GenomicRanges-comparison
elementMetadata,GIntervalTree-method	GIntervalTree-class
elementMetadata,GRangesList-method	GRangesList-class
elementMetadata,SummarizedExperiment-method	SummarizedExperiment-class
elementMetadata<-,GenomicRanges-method	GRanges-class
elementMetadata<-,GRangesList-method	GRangesList-class
elementMetadata<-,SummarizedExperiment-method	SummarizedExperiment-class
end,GenomicRanges-method	GRanges-class
end,GIntervalTree-method	GIntervalTree-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
findOverlaps	findOverlaps-methods
findOverlaps,GenomicRanges,GenomicRanges-method	findOverlaps-methods
findOverlaps,GenomicRanges,GIntervalTree-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,SummarizedExperiment-method	SummarizedExperiment-class
findOverlaps,SummarizedExperiment,Vector-method	SummarizedExperiment-class
findOverlaps,Vector,SummarizedExperiment-method	SummarizedExperiment-class
findOverlaps-methods	findOverlaps-methods
flank	intra-range-methods
flank,GenomicRanges-method	intra-range-methods
flank,GRangesList-method	intra-range-methods
flank,SummarizedExperiment-method	SummarizedExperiment-class
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
gaps	inter-range-methods
gaps,GenomicRanges-method	inter-range-methods
GenomicRanges	GRanges-class
GenomicRanges-class	GRanges-class
GenomicRanges-comparison	GenomicRanges-comparison
GenomicRanges-deprecated	deprecated
GenomicRangesList	GenomicRangesList-class
GenomicRangesList-class	GenomicRangesList-class
GenomicRangesORGRangesList-class	GRanges-class
GenomicRangesORmissing-class	GRanges-class
GIntervalTree	GIntervalTree-class
GIntervalTree-class	GIntervalTree-class
GRanges	GRanges-class
granges	range-squeezers
granges,GenomicRanges-method	GRanges-class
granges,GRangesMapping-method	GRangesMapping-class
granges,SummarizedExperiment-method	SummarizedExperiment-class
GRanges-class	GRanges-class
GRangesList	GRangesList-class
GRangesList-class	GRangesList-class
GRangesMapping	GRangesMapping-class
GRangesMapping-class	GRangesMapping-class
grglist	range-squeezers
hits	GRangesMapping-class
inter-range-methods	inter-range-methods
intersect,GRanges,GRanges-method	setops-methods
intra-range-methods	intra-range-methods
isDisjoint	inter-range-methods
isDisjoint,GenomicRanges-method	inter-range-methods
isDisjoint,GRangesList-method	inter-range-methods
isDisjoint,SummarizedExperiment-method	SummarizedExperiment-class
length,GenomicRanges-method	GRanges-class
length,GRangesMapping-method	GRangesMapping-class
makeGRangesFromDataFrame	makeGRangesFromDataFrame
makeGRangesListFromFeatureFragments	GRangesList-class
makeSeqnameIds	deprecated
map,GenomicRanges,GRangesList-method	map-methods
map-methods	map-methods
mapCoords	mapCoords-methods
mapCoords,GenomicRanges,GRangesList-method	mapCoords-methods
mapCoords-methods	mapCoords-methods
match,GenomicRanges,GenomicRanges-method	GenomicRanges-comparison
mcols,SummarizedExperiment-method	SummarizedExperiment-class
mcols<-,SummarizedExperiment-method	SummarizedExperiment-class
names,GenomicRanges-method	GRanges-class
names,GIntervalTree-method	GIntervalTree-class
names<-,GenomicRanges-method	GRanges-class
narrow	intra-range-methods
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
Ops,GenomicRanges,numeric-method	intra-range-methods
order,GenomicRanges-method	GenomicRanges-comparison
order,SummarizedExperiment-method	SummarizedExperiment-class
overlapsAny	findOverlaps-methods
overlapsAny,GenomicRanges,GenomicRanges-method	findOverlaps-methods
overlapsAny,GenomicRanges,GRangesList-method	findOverlaps-methods
overlapsAny,GenomicRanges,RangedData-method	findOverlaps-methods
overlapsAny,GenomicRanges,RangesList-method	findOverlaps-methods
overlapsAny,GRangesList,GenomicRanges-method	findOverlaps-methods
overlapsAny,GRangesList,GRangesList-method	findOverlaps-methods
overlapsAny,GRangesList,RangedData-method	findOverlaps-methods
overlapsAny,GRangesList,RangesList-method	findOverlaps-methods
overlapsAny,RangedData,GenomicRanges-method	findOverlaps-methods
overlapsAny,RangedData,GRangesList-method	findOverlaps-methods
overlapsAny,RangesList,GenomicRanges-method	findOverlaps-methods
overlapsAny,RangesList,GRangesList-method	findOverlaps-methods
overlapsAny,SummarizedExperiment,SummarizedExperiment-method	SummarizedExperiment-class
overlapsAny,SummarizedExperiment,Vector-method	SummarizedExperiment-class
overlapsAny,Vector,SummarizedExperiment-method	SummarizedExperiment-class
pgap,GRanges,GRanges-method	setops-methods
phicoef	phicoef
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
promoters	intra-range-methods
promoters,GenomicRanges-method	intra-range-methods
promoters,GRangesList-method	intra-range-methods
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
queryHits,GRangesMapping-method	GRangesMapping-class
range	inter-range-methods
range,GenomicRanges-method	inter-range-methods
range,GRangesList-method	inter-range-methods
range-squeezers	range-squeezers
ranges,GIntervalTree-method	GIntervalTree-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
rbind,SummarizedExperiment-method	SummarizedExperiment-class
reduce	inter-range-methods
reduce,GenomicRanges-method	inter-range-methods
reduce,GRangesList-method	inter-range-methods
relistToClass,GRanges-method	GRangesList-class
resize	intra-range-methods
resize,GenomicRanges-method	intra-range-methods
resize,GRangesList-method	intra-range-methods
resize,SummarizedExperiment-method	SummarizedExperiment-class
restrict	intra-range-methods
restrict,GenomicRanges-method	intra-range-methods
restrict,GRangesList-method	intra-range-methods
restrict,SummarizedExperiment-method	SummarizedExperiment-class
rglist	range-squeezers
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,GIntervalTree-method	GIntervalTree-class
score,GRangesList-method	GRangesList-class
score<-,GenomicRanges-method	GRanges-class
score<-,GRangesList-method	GRangesList-class
seqinfo,GIntervalTree-method	GIntervalTree-class
seqinfo,GRanges-method	GRanges-class
seqinfo,GRangesList-method	GRangesList-class
seqinfo,SummarizedExperiment-method	SummarizedExperiment-class
seqinfo<-,GenomicRanges-method	GRanges-class
seqinfo<-,GRangesList-method	GRangesList-class
seqinfo<-,SummarizedExperiment-method	SummarizedExperiment-class
seqnames,GIntervalTree-method	GIntervalTree-class
seqnames,GRanges-method	GRanges-class
seqnames,GRangesList-method	GRangesList-class
seqnames,SummarizedExperiment-method	SummarizedExperiment-class
seqnames<-,GenomicRanges-method	GRanges-class
seqnames<-,GRangesList-method	GRangesList-class
setdiff,GRanges,GRanges-method	setops-methods
setops-methods	setops-methods
shift	intra-range-methods
shift,GenomicRanges-method	intra-range-methods
shift,GRangesList-method	intra-range-methods
shift,SummarizedExperiment-method	SummarizedExperiment-class
show,GenomicRanges-method	GRanges-class
show,GIntervalTree-method	GIntervalTree-class
show,GRangesList-method	GRangesList-class
show,SummarizedExperiment-method	SummarizedExperiment-class
SimpleGenomicRangesList-class	GenomicRangesList-class
sort,GenomicRanges-method	GenomicRanges-comparison
sort,SummarizedExperiment-method	SummarizedExperiment-class
sort.GenomicRanges	GenomicRanges-comparison
split,SummarizedExperiment,ANY-method	SummarizedExperiment-class
split,SummarizedExperiment-method	SummarizedExperiment-class
splitAsListReturnedClass,GRanges-method	GRangesList-class
start,GenomicRanges-method	GRanges-class
start,GIntervalTree-method	GIntervalTree-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,GIntervalTree-method	GIntervalTree-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,NULL-method	strand-utils
strand,Rle-method	strand-utils
strand,SummarizedExperiment-method	SummarizedExperiment-class
strand-utils	strand-utils
strand<-,DataTable,ANY-method	strand-utils
strand<-,GenomicRanges,ANY-method	GRanges-class
strand<-,GRangesList,ANY-method	GRangesList-class
strand<-,GRangesList,character-method	GRangesList-class
strand<-,SummarizedExperiment,ANY-method	SummarizedExperiment-class
subjectHits,GRangesMapping-method	GRangesMapping-class
subset,SummarizedExperiment-method	SummarizedExperiment-class
subsetByOverlaps	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
subsetByOverlaps,SummarizedExperiment,SummarizedExperiment-method	SummarizedExperiment-class
subsetByOverlaps,SummarizedExperiment,Vector-method	SummarizedExperiment-class
subsetByOverlaps,Vector,SummarizedExperiment-method	SummarizedExperiment-class
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
tile,GenomicRanges-method	GRanges-class
tile,GenomicRanges-method	tile-methods
tile-methods	tile-methods
tileGenome	tileGenome
trim,GenomicRanges-method	intra-range-methods
union,GRanges,GRanges-method	setops-methods
updateObject,GRanges-method	GRanges-class
updateObject,GRangesList-method	GRangesList-class
updateObject,SummarizedExperiment-method	SummarizedExperiment-class
values,SummarizedExperiment-method	SummarizedExperiment-class
values<-,SummarizedExperiment-method	SummarizedExperiment-class
width,GenomicRanges-method	GRanges-class
width,GIntervalTree-method	GIntervalTree-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
[,GenomicRanges,ANY-method	GRanges-class
[,GIntervalTree,ANY-method	GIntervalTree-class
[,GRangesList,ANY-method	GRangesList-class
[,List,GenomicRanges-method	GRanges-class
[,list,GenomicRanges-method	GRanges-class
[,SummarizedExperiment,ANY-method	SummarizedExperiment-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
[[,SummarizedExperiment,ANY,missing-method	SummarizedExperiment-class
[[<-,GRangesList,ANY,ANY-method	GRangesList-class
[[<-,SummarizedExperiment,ANY,missing,ANY-method	SummarizedExperiment-class
[[<-,SummarizedExperiment,ANY,missing-method	SummarizedExperiment-class
