$,SummarizedExperiment0-method	SummarizedExperiment0-class
$<-,SummarizedExperiment0-method	SummarizedExperiment0-class
assay	SummarizedExperiment0-class
assay,SummarizedExperiment0,character-method	SummarizedExperiment0-class
assay,SummarizedExperiment0,missing-method	SummarizedExperiment0-class
assay,SummarizedExperiment0,numeric-method	SummarizedExperiment0-class
assay<-	SummarizedExperiment0-class
assay<-,SummarizedExperiment0,character,matrix-method	SummarizedExperiment0-class
assay<-,SummarizedExperiment0,missing,matrix-method	SummarizedExperiment0-class
assay<-,SummarizedExperiment0,numeric,matrix-method	SummarizedExperiment0-class
assayNames	SummarizedExperiment0-class
assayNames,SummarizedExperiment0-method	SummarizedExperiment0-class
assayNames<-	SummarizedExperiment0-class
assayNames<-,SummarizedExperiment0,character-method	SummarizedExperiment0-class
Assays	Assays-class
assays	SummarizedExperiment0-class
assays,SummarizedExperiment0-method	SummarizedExperiment0-class
Assays-class	Assays-class
assays<-	SummarizedExperiment0-class
assays<-,SummarizedExperiment0,list-method	SummarizedExperiment0-class
assays<-,SummarizedExperiment0,SimpleList-method	SummarizedExperiment0-class
AssaysInEnv	Assays-class
AssaysInEnv-class	Assays-class
cbind,Assays-method	Assays-class
cbind,SummarizedExperiment0-method	SummarizedExperiment0-class
class:Assays	Assays-class
class:AssaysInEnv	Assays-class
class:RangedSummarizedExperiment	RangedSummarizedExperiment-class
class:ShallowSimpleListAssays	Assays-class
class:SimpleListAssays	Assays-class
class:SummarizedExperiment0	SummarizedExperiment0-class
coerce,AssaysInEnv,SimpleList-method	Assays-class
coerce,ExpressionSet,RangedSummarizedExperiment-method	makeSummarizedExperimentFromExpressionSet
coerce,RangedSummarizedExperiment,ExpressionSet-method	makeSummarizedExperimentFromExpressionSet
coerce,RangedSummarizedExperiment,SummarizedExperiment0-method	RangedSummarizedExperiment-class
coerce,ShallowSimpleListAssays,SimpleList-method	Assays-class
coerce,SimpleList,AssaysInEnv-method	Assays-class
coerce,SimpleList,ShallowSimpleListAssays-method	Assays-class
coerce,SummarizedExperiment0,ExpressionSet-method	makeSummarizedExperimentFromExpressionSet
coerce,SummarizedExperiment0,RangedSummarizedExperiment-method	RangedSummarizedExperiment-class
colData	SummarizedExperiment0-class
colData,SummarizedExperiment0-method	SummarizedExperiment0-class
colData<-	SummarizedExperiment0-class
colData<-,SummarizedExperiment0,DataFrame-method	SummarizedExperiment0-class
Compare,ANY,RangedSummarizedExperiment-method	RangedSummarizedExperiment-class
compare,ANY,RangedSummarizedExperiment-method	RangedSummarizedExperiment-class
Compare,RangedSummarizedExperiment,ANY-method	RangedSummarizedExperiment-class
compare,RangedSummarizedExperiment,ANY-method	RangedSummarizedExperiment-class
Compare,RangedSummarizedExperiment,RangedSummarizedExperiment-method	RangedSummarizedExperiment-class
compare,RangedSummarizedExperiment,RangedSummarizedExperiment-method	RangedSummarizedExperiment-class
countOverlaps	findOverlaps-methods
countOverlaps,RangedSummarizedExperiment,RangedSummarizedExperiment-method	findOverlaps-methods
countOverlaps,RangedSummarizedExperiment,Vector-method	findOverlaps-methods
countOverlaps,Vector,RangedSummarizedExperiment-method	findOverlaps-methods
coverage	coverage-methods
coverage,RangedSummarizedExperiment-method	coverage-methods
coverage-methods	coverage-methods
dim,Assays-method	Assays-class
dim,SummarizedExperiment0-method	SummarizedExperiment0-class
dimnames,RangedSummarizedExperiment-method	RangedSummarizedExperiment-class
dimnames,SummarizedExperiment0-method	SummarizedExperiment0-class
dimnames<-,RangedSummarizedExperiment,list-method	RangedSummarizedExperiment-class
dimnames<-,SummarizedExperiment0,list-method	SummarizedExperiment0-class
dimnames<-,SummarizedExperiment0,NULL-method	SummarizedExperiment0-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
exptData,SummarizedExperiment0-method	SummarizedExperiment0-class
exptData<-,SummarizedExperiment0-method	SummarizedExperiment0-class
extractROWS,SummarizedExperiment0,ANY-method	SummarizedExperiment0-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
isDisjoint	inter-range-methods
isDisjoint,RangedSummarizedExperiment-method	inter-range-methods
KALLISTO_ASSAYS	readKallisto
length,Assays-method	Assays-class
length,AssaysInEnv-method	Assays-class
length,SummarizedExperiment0-method	SummarizedExperiment0-class
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,SummarizedExperiment0-method	SummarizedExperiment0-class
names<-,Assays-method	Assays-class
names<-,AssaysInEnv-method	Assays-class
names<-,RangedSummarizedExperiment-method	RangedSummarizedExperiment-class
names<-,SummarizedExperiment0-method	SummarizedExperiment0-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
overlapsAny	findOverlaps-methods
overlapsAny,RangedSummarizedExperiment,RangedSummarizedExperiment-method	findOverlaps-methods
overlapsAny,RangedSummarizedExperiment,Vector-method	findOverlaps-methods
overlapsAny,Vector,RangedSummarizedExperiment-method	findOverlaps-methods
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,SummarizedExperiment0-method	SummarizedExperiment0-class
readKallisto	readKallisto
readKallistoBootstrap	readKallisto
replaceROWS,SummarizedExperiment0-method	SummarizedExperiment0-class
resize	intra-range-methods
resize,RangedSummarizedExperiment-method	intra-range-methods
restrict	intra-range-methods
restrict,RangedSummarizedExperiment-method	intra-range-methods
rowRanges	RangedSummarizedExperiment-class
rowRanges,RangedSummarizedExperiment-method	RangedSummarizedExperiment-class
rowRanges<-	RangedSummarizedExperiment-class
rowRanges<-,SummarizedExperiment0,GenomicRanges-method	RangedSummarizedExperiment-class
rowRanges<-,SummarizedExperiment0,GRangesList-method	RangedSummarizedExperiment-class
seqinfo,RangedSummarizedExperiment-method	RangedSummarizedExperiment-class
seqinfo<-,RangedSummarizedExperiment-method	RangedSummarizedExperiment-class
seqnames,RangedSummarizedExperiment-method	RangedSummarizedExperiment-class
ShallowSimpleListAssays	Assays-class
ShallowSimpleListAssays-class	Assays-class
shift	intra-range-methods
shift,RangedSummarizedExperiment-method	intra-range-methods
show,SummarizedExperiment0-method	SummarizedExperiment0-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
subsetByOverlaps	findOverlaps-methods
subsetByOverlaps,RangedSummarizedExperiment,RangedSummarizedExperiment-method	findOverlaps-methods
subsetByOverlaps,RangedSummarizedExperiment,Vector-method	findOverlaps-methods
subsetByOverlaps,Vector,RangedSummarizedExperiment-method	findOverlaps-methods
SummarizedExperiment	RangedSummarizedExperiment-class
SummarizedExperiment,list-method	RangedSummarizedExperiment-class
SummarizedExperiment,matrix-method	RangedSummarizedExperiment-class
SummarizedExperiment,missing-method	RangedSummarizedExperiment-class
SummarizedExperiment,SimpleList-method	RangedSummarizedExperiment-class
SummarizedExperiment0	SummarizedExperiment0-class
SummarizedExperiment0-class	SummarizedExperiment0-class
trim,RangedSummarizedExperiment-method	intra-range-methods
updateObject,RangedSummarizedExperiment-method	RangedSummarizedExperiment-class
width,RangedSummarizedExperiment-method	RangedSummarizedExperiment-class
width<-,RangedSummarizedExperiment-method	RangedSummarizedExperiment-class
[,Assays,ANY-method	Assays-class
[,SummarizedExperiment0,ANY-method	SummarizedExperiment0-class
[,SummarizedExperiment0-method	SummarizedExperiment0-class
[<-,Assays,ANY,ANY,ANY-method	Assays-class
[<-,SummarizedExperiment0,ANY,ANY,SummarizedExperiment0-method	SummarizedExperiment0-class
[[,Assays,ANY,ANY-method	Assays-class
[[,AssaysInEnv,ANY,ANY-method	Assays-class
[[,SummarizedExperiment0,ANY,missing-method	SummarizedExperiment0-class
[[<-,Assays,ANY,ANY-method	Assays-class
[[<-,AssaysInEnv,ANY,ANY-method	Assays-class
[[<-,SummarizedExperiment0,ANY,missing-method	SummarizedExperiment0-class
