$,SummarizedExperiment-method	SummarizedExperiment-class
$<-,SummarizedExperiment-method	SummarizedExperiment-class
acbind,Matrix-method	Assays-class
arbind,Matrix-method	Assays-class
assay	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-method	SummarizedExperiment-class
assay<-,SummarizedExperiment,missing-method	SummarizedExperiment-class
assay<-,SummarizedExperiment,numeric-method	SummarizedExperiment-class
assayNames	SummarizedExperiment-class
assayNames,SummarizedExperiment-method	SummarizedExperiment-class
assayNames<-	SummarizedExperiment-class
assayNames<-,SummarizedExperiment,character-method	SummarizedExperiment-class
Assays	Assays-class
assays	SummarizedExperiment-class
assays,SummarizedExperiment-method	SummarizedExperiment-class
Assays-class	Assays-class
assays<-	SummarizedExperiment-class
assays<-,SummarizedExperiment,list-method	SummarizedExperiment-class
assays<-,SummarizedExperiment,SimpleList-method	SummarizedExperiment-class
AssaysInEnv	Assays-class
AssaysInEnv-class	Assays-class
cbind,Assays-method	Assays-class
cbind,SummarizedExperiment-method	SummarizedExperiment-class
class:Assays	Assays-class
class:AssaysInEnv	Assays-class
class:RangedSummarizedExperiment	RangedSummarizedExperiment-class
class:ShallowData	Assays-class
class:ShallowSimpleListAssays	Assays-class
class:SimpleListAssays	Assays-class
class:SummarizedExperiment	SummarizedExperiment-class
coerce,AssaysInEnv,SimpleList-method	Assays-class
coerce,ExpressionSet,RangedSummarizedExperiment-method	makeSummarizedExperimentFromExpressionSet
coerce,RangedSummarizedExperiment,ExpressionSet-method	makeSummarizedExperimentFromExpressionSet
coerce,RangedSummarizedExperiment,SummarizedExperiment-method	RangedSummarizedExperiment-class
coerce,ShallowSimpleListAssays,SimpleList-method	Assays-class
coerce,SimpleList,AssaysInEnv-method	Assays-class
coerce,SimpleList,ShallowSimpleListAssays-method	Assays-class
coerce,SummarizedExperiment,ExpressionSet-method	makeSummarizedExperimentFromExpressionSet
coerce,SummarizedExperiment,RangedSummarizedExperiment-method	RangedSummarizedExperiment-class
colData	SummarizedExperiment-class
colData,SummarizedExperiment-method	SummarizedExperiment-class
colData<-	SummarizedExperiment-class
colData<-,SummarizedExperiment,DataFrame-method	SummarizedExperiment-class
Compare,ANY,RangedSummarizedExperiment-method	RangedSummarizedExperiment-class
Compare,RangedSummarizedExperiment,ANY-method	RangedSummarizedExperiment-class
Compare,RangedSummarizedExperiment,RangedSummarizedExperiment-method	RangedSummarizedExperiment-class
coverage	coverage-methods
coverage,RangedSummarizedExperiment-method	coverage-methods
coverage-methods	coverage-methods
dim,Assays-method	Assays-class
dim,SummarizedExperiment-method	SummarizedExperiment-class
dimnames,RangedSummarizedExperiment-method	RangedSummarizedExperiment-class
dimnames,SummarizedExperiment-method	SummarizedExperiment-class
dimnames<-,RangedSummarizedExperiment,list-method	RangedSummarizedExperiment-class
dimnames<-,SummarizedExperiment,list-method	SummarizedExperiment-class
dimnames<-,SummarizedExperiment,NULL-method	SummarizedExperiment-class
disjointBins	inter-range-methods
disjointBins,RangedSummarizedExperiment-method	inter-range-methods
distance	nearest-methods
distance,ANY,RangedSummarizedExperiment-method	nearest-methods
distance,RangedSummarizedExperiment,ANY-method	nearest-methods
distance,RangedSummarizedExperiment,RangedSummarizedExperiment-method	nearest-methods
distanceToNearest	nearest-methods
distanceToNearest,ANY,RangedSummarizedExperiment-method	nearest-methods
distanceToNearest,RangedSummarizedExperiment,ANY-method	nearest-methods
distanceToNearest,RangedSummarizedExperiment,RangedSummarizedExperiment-method	nearest-methods
duplicated,RangedSummarizedExperiment-method	RangedSummarizedExperiment-class
elementMetadata,RangedSummarizedExperiment-method	RangedSummarizedExperiment-class
elementMetadata<-,RangedSummarizedExperiment-method	RangedSummarizedExperiment-class
end,RangedSummarizedExperiment-method	RangedSummarizedExperiment-class
end<-,RangedSummarizedExperiment-method	RangedSummarizedExperiment-class
extractROWS,SummarizedExperiment,ANY-method	SummarizedExperiment-class
findOverlaps	findOverlaps-methods
findOverlaps,RangedSummarizedExperiment,RangedSummarizedExperiment-method	findOverlaps-methods
findOverlaps,RangedSummarizedExperiment,Vector-method	findOverlaps-methods
findOverlaps,Vector,RangedSummarizedExperiment-method	findOverlaps-methods
findOverlaps-methods	findOverlaps-methods
flank	intra-range-methods
flank,RangedSummarizedExperiment-method	intra-range-methods
follow	nearest-methods
follow,ANY,RangedSummarizedExperiment-method	nearest-methods
follow,RangedSummarizedExperiment,ANY-method	nearest-methods
follow,RangedSummarizedExperiment,RangedSummarizedExperiment-method	nearest-methods
geneRangeMapper	makeSummarizedExperimentFromExpressionSet
granges,RangedSummarizedExperiment-method	RangedSummarizedExperiment-class
inter-range-methods	inter-range-methods
intra-range-methods	intra-range-methods
is.unsorted,RangedSummarizedExperiment-method	RangedSummarizedExperiment-class
isDisjoint	inter-range-methods
isDisjoint,RangedSummarizedExperiment-method	inter-range-methods
KALLISTO_ASSAYS	readKallisto
length,Assays-method	Assays-class
length,AssaysInEnv-method	Assays-class
length,SummarizedExperiment-method	SummarizedExperiment-class
loadHDF5SummarizedExperiment	saveHDF5SummarizedExperiment
makeSummarizedExperimentFromDataFrame	makeSummarizedExperimentFromDataFrame
makeSummarizedExperimentFromExpressionSet	makeSummarizedExperimentFromExpressionSet
mcols,RangedSummarizedExperiment-method	RangedSummarizedExperiment-class
mcols<-,RangedSummarizedExperiment-method	RangedSummarizedExperiment-class
naiveRangeMapper	makeSummarizedExperimentFromExpressionSet
names,Assays-method	Assays-class
names,AssaysInEnv-method	Assays-class
names,RangedSummarizedExperiment-method	RangedSummarizedExperiment-class
names,SummarizedExperiment-method	SummarizedExperiment-class
names<-,Assays-method	Assays-class
names<-,AssaysInEnv-method	Assays-class
names<-,RangedSummarizedExperiment-method	RangedSummarizedExperiment-class
names<-,SummarizedExperiment-method	SummarizedExperiment-class
narrow	intra-range-methods
narrow,RangedSummarizedExperiment-method	intra-range-methods
nearest	nearest-methods
nearest,ANY,RangedSummarizedExperiment-method	nearest-methods
nearest,RangedSummarizedExperiment,ANY-method	nearest-methods
nearest,RangedSummarizedExperiment,RangedSummarizedExperiment-method	nearest-methods
nearest-methods	nearest-methods
order,RangedSummarizedExperiment-method	RangedSummarizedExperiment-class
pcompare,ANY,RangedSummarizedExperiment-method	RangedSummarizedExperiment-class
pcompare,RangedSummarizedExperiment,ANY-method	RangedSummarizedExperiment-class
pcompare,RangedSummarizedExperiment,RangedSummarizedExperiment-method	RangedSummarizedExperiment-class
precede	nearest-methods
precede,ANY,RangedSummarizedExperiment-method	nearest-methods
precede,RangedSummarizedExperiment,ANY-method	nearest-methods
precede,RangedSummarizedExperiment,RangedSummarizedExperiment-method	nearest-methods
probeRangeMapper	makeSummarizedExperimentFromExpressionSet
promoters	intra-range-methods
promoters,RangedSummarizedExperiment-method	intra-range-methods
RangedSummarizedExperiment	RangedSummarizedExperiment-class
RangedSummarizedExperiment-class	RangedSummarizedExperiment-class
ranges,RangedSummarizedExperiment-method	RangedSummarizedExperiment-class
ranges<-,RangedSummarizedExperiment-method	RangedSummarizedExperiment-class
rank,RangedSummarizedExperiment-method	RangedSummarizedExperiment-class
rbind,Assays-method	Assays-class
rbind,SummarizedExperiment-method	SummarizedExperiment-class
readKallisto	readKallisto
readKallistoBootstrap	readKallisto
realize,SummarizedExperiment-method	SummarizedExperiment-class
replaceROWS,SummarizedExperiment-method	SummarizedExperiment-class
resize	intra-range-methods
resize,RangedSummarizedExperiment-method	intra-range-methods
restrict	intra-range-methods
restrict,RangedSummarizedExperiment-method	intra-range-methods
rowData	SummarizedExperiment-class
rowData,SummarizedExperiment-method	SummarizedExperiment-class
rowData<-	SummarizedExperiment-class
rowData<-,SummarizedExperiment-method	SummarizedExperiment-class
rowRanges	RangedSummarizedExperiment-class
rowRanges,RangedSummarizedExperiment-method	RangedSummarizedExperiment-class
rowRanges<-	RangedSummarizedExperiment-class
rowRanges<-,SummarizedExperiment,GenomicRanges-method	RangedSummarizedExperiment-class
rowRanges<-,SummarizedExperiment,GRangesList-method	RangedSummarizedExperiment-class
saveHDF5SummarizedExperiment	saveHDF5SummarizedExperiment
seqinfo,RangedSummarizedExperiment-method	RangedSummarizedExperiment-class
seqinfo<-,RangedSummarizedExperiment-method	RangedSummarizedExperiment-class
seqnames,RangedSummarizedExperiment-method	RangedSummarizedExperiment-class
ShallowData	Assays-class
ShallowData-class	Assays-class
ShallowSimpleListAssays	Assays-class
ShallowSimpleListAssays-class	Assays-class
shift	intra-range-methods
shift,RangedSummarizedExperiment-method	intra-range-methods
show,SummarizedExperiment-method	SummarizedExperiment-class
SimpleListAssays	Assays-class
SimpleListAssays-class	Assays-class
sort,RangedSummarizedExperiment-method	RangedSummarizedExperiment-class
split,RangedSummarizedExperiment,ANY-method	RangedSummarizedExperiment-class
split,RangedSummarizedExperiment-method	RangedSummarizedExperiment-class
start,RangedSummarizedExperiment-method	RangedSummarizedExperiment-class
start<-,RangedSummarizedExperiment-method	RangedSummarizedExperiment-class
strand,RangedSummarizedExperiment-method	RangedSummarizedExperiment-class
strand<-,RangedSummarizedExperiment,ANY-method	RangedSummarizedExperiment-class
subset,RangedSummarizedExperiment-method	RangedSummarizedExperiment-class
SummarizedExperiment	RangedSummarizedExperiment-class
SummarizedExperiment,ANY-method	RangedSummarizedExperiment-class
SummarizedExperiment,list-method	RangedSummarizedExperiment-class
SummarizedExperiment,missing-method	RangedSummarizedExperiment-class
SummarizedExperiment,SimpleList-method	RangedSummarizedExperiment-class
SummarizedExperiment-class	SummarizedExperiment-class
trim,RangedSummarizedExperiment-method	intra-range-methods
updateObject,SummarizedExperiment-method	RangedSummarizedExperiment-class
width,RangedSummarizedExperiment-method	RangedSummarizedExperiment-class
width<-,RangedSummarizedExperiment-method	RangedSummarizedExperiment-class
[,Assays,ANY,ANY,ANY-method	Assays-class
[,Assays,ANY-method	Assays-class
[,SummarizedExperiment,ANY,ANY,ANY-method	SummarizedExperiment-class
[,SummarizedExperiment,ANY-method	SummarizedExperiment-class
[,SummarizedExperiment-method	SummarizedExperiment-class
[<-,Assays,ANY,ANY,ANY-method	Assays-class
[<-,SummarizedExperiment,ANY,ANY,SummarizedExperiment-method	SummarizedExperiment-class
[[,Assays,ANY,ANY-method	Assays-class
[[,AssaysInEnv,ANY,ANY-method	Assays-class
[[,SummarizedExperiment,ANY,missing-method	SummarizedExperiment-class
[[<-,Assays,ANY,ANY-method	Assays-class
[[<-,AssaysInEnv,ANY,ANY-method	Assays-class
[[<-,SummarizedExperiment,ANY,missing-method	SummarizedExperiment-class
