r-bioc-genomicranges 1.14.3-1 / usr / lib / R / site-library / GenomicRanges / help / AnIndex

$,GenomicRanges-method	GRanges-class
$,SummarizedExperiment-method	SummarizedExperiment-class
$<-,GenomicRanges-method	GRanges-class
$<-,SummarizedExperiment,ANY-method	SummarizedExperiment-class
$<-,SummarizedExperiment-method	SummarizedExperiment-class
%in%,GAlignmentPairs,Vector-method	findOverlaps-methods
%in%,GAlignments,GAlignments-method	findOverlaps-methods
%in%,GAlignments,Vector-method	findOverlaps-methods
%in%,GAlignmentsList,GAlignmentsList-method	findOverlaps-methods
%in%,GAlignmentsList,Vector-method	findOverlaps-methods
%in%,GenomicRanges,GenomicRanges-method	GenomicRanges-comparison
%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
%in%,SummarizedExperiment,SummarizedExperiment-method	SummarizedExperiment-class
%in%,SummarizedExperiment,Vector-method	SummarizedExperiment-class
%in%,Vector,GAlignmentPairs-method	findOverlaps-methods
%in%,Vector,GAlignments-method	findOverlaps-methods
%in%,Vector,GAlignmentsList-method	findOverlaps-methods
%in%,Vector,SummarizedExperiment-method	SummarizedExperiment-class
<=,GenomicRanges,GenomicRanges-method	GenomicRanges-comparison
==,GenomicRanges,GenomicRanges-method	GenomicRanges-comparison
as.data.frame,GAlignments-method	GAlignments-class
as.data.frame,GAlignmentsList-method	GAlignmentsList-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,GAlignmentPairs-method	GAlignmentPairs-class
c,GAlignments-method	GAlignments-class
c,GAlignmentsList-method	GAlignmentsList-class
c,GenomicRanges-method	GRanges-class
cbind,SummarizedExperiment-method	SummarizedExperiment-class
checkConstraint	constraint
cigar	GAlignments-class
cigar,GAlignments-method	GAlignments-class
cigar,GAlignmentsList-method	GAlignmentsList-class
cigar-utils	cigar-utils
cigarNarrow	cigar-utils
cigarOpTable	cigar-utils
cigarQNarrow	cigar-utils
cigarRangesAlongPairwiseSpace	cigar-utils
cigarRangesAlongQuerySpace	cigar-utils
cigarRangesAlongReferenceSpace	cigar-utils
cigarToCigarTable	cigar-utils
cigarToIRanges	cigar-utils
cigarToIRangesListByAlignment	cigar-utils
cigarToIRangesListByRName	cigar-utils
cigarToQWidth	cigar-utils
cigarToRleList	cigar-utils
cigarToWidth	cigar-utils
cigarWidthAlongPairwiseSpace	cigar-utils
cigarWidthAlongQuerySpace	cigar-utils
cigarWidthAlongReferenceSpace	cigar-utils
CIGAR_OPS	cigar-utils
class:Constraint	constraint
class:ConstraintORNULL	constraint
class:GAlignmentPairs	GAlignmentPairs-class
class:GAlignments	GAlignments-class
class:GAlignmentsList	GAlignmentsList-class
class:GappedAlignmentPairs	GAlignmentPairs-class
class:GappedAlignments	GAlignments-class
class:GenomicRanges	GRanges-class
class:GenomicRangesList	GenomicRangesList-class
class:GIntervalTree	GIntervalTree-class
class:GRanges	GRanges-class
class:GRangesList	GRangesList-class
class:Seqinfo	Seqinfo-class
class:SimpleGenomicRangesList	GenomicRangesList-class
coerce,data.frame,GRanges-method	makeGRangesFromDataFrame
coerce,DataFrame,GRanges-method	makeGRangesFromDataFrame
coerce,GAlignmentPairs,GAlignments-method	GAlignmentPairs-class
coerce,GAlignmentPairs,GAlignmentsList-method	GAlignmentsList-class
coerce,GAlignmentPairs,GRanges-method	GAlignmentPairs-class
coerce,GAlignmentPairs,GRangesList-method	GAlignmentPairs-class
coerce,GAlignments,GRanges-method	GAlignments-class
coerce,GAlignments,GRangesList-method	GAlignments-class
coerce,GAlignments,Ranges-method	GAlignments-class
coerce,GAlignments,RangesList-method	GAlignments-class
coerce,GAlignmentsList,GRanges-method	GAlignmentsList-class
coerce,GAlignmentsList,GRangesList-method	GAlignmentsList-class
coerce,GAlignmentsList,Ranges-method	GAlignmentsList-class
coerce,GAlignmentsList,RangesList-method	GAlignmentsList-class
coerce,GenomicRanges,GAlignments-method	GRanges-class
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,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
countMatches,GAlignmentPairs,Vector-method	findOverlaps-methods
countMatches,GAlignments,GAlignments-method	findOverlaps-methods
countMatches,GAlignments,Vector-method	findOverlaps-methods
countMatches,GAlignmentsList,GAlignmentsList-method	findOverlaps-methods
countMatches,GAlignmentsList,Vector-method	findOverlaps-methods
countMatches,GenomicRanges,GenomicRanges-method	GenomicRanges-comparison
countMatches,GenomicRanges,GRangesList-method	findOverlaps-methods
countMatches,GenomicRanges,RangedData-method	findOverlaps-methods
countMatches,GenomicRanges,RangesList-method	findOverlaps-methods
countMatches,GRangesList,GenomicRanges-method	findOverlaps-methods
countMatches,GRangesList,GRangesList-method	findOverlaps-methods
countMatches,GRangesList,RangedData-method	findOverlaps-methods
countMatches,GRangesList,RangesList-method	findOverlaps-methods
countMatches,RangedData,GenomicRanges-method	findOverlaps-methods
countMatches,RangedData,GRangesList-method	findOverlaps-methods
countMatches,RangesList,GenomicRanges-method	findOverlaps-methods
countMatches,RangesList,GRangesList-method	findOverlaps-methods
countMatches,Vector,GAlignmentPairs-method	findOverlaps-methods
countMatches,Vector,GAlignments-method	findOverlaps-methods
countMatches,Vector,GAlignmentsList-method	findOverlaps-methods
countOverlaps,GAlignmentPairs,GAlignmentPairs-method	findOverlaps-methods
countOverlaps,GAlignmentPairs,Vector-method	findOverlaps-methods
countOverlaps,GAlignments,GAlignments-method	findOverlaps-methods
countOverlaps,GAlignments,GenomicRanges-method	findOverlaps-methods
countOverlaps,GAlignments,GRangesList-method	findOverlaps-methods
countOverlaps,GAlignments,Vector-method	findOverlaps-methods
countOverlaps,GAlignmentsList,GAlignmentsList-method	findOverlaps-methods
countOverlaps,GAlignmentsList,Vector-method	findOverlaps-methods
countOverlaps,GenomicRanges,GAlignments-method	findOverlaps-methods
countOverlaps,GenomicRanges,GenomicRanges-method	findOverlaps-methods
countOverlaps,GenomicRanges,Vector-method	findOverlaps-methods
countOverlaps,GRanges,GRangesList-method	findOverlaps-methods
countOverlaps,GRangesList,GAlignments-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,GAlignmentPairs-method	findOverlaps-methods
countOverlaps,Vector,GAlignments-method	findOverlaps-methods
countOverlaps,Vector,GAlignmentsList-method	findOverlaps-methods
countOverlaps,Vector,GenomicRanges-method	findOverlaps-methods
countOverlaps,Vector,GRangesList-method	findOverlaps-methods
countOverlaps,Vector,SummarizedExperiment-method	SummarizedExperiment-class
coverage,GAlignmentPairs-method	coverage-methods
coverage,GAlignments-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
dropSeqlevels	seqlevels-utils
duplicated,GenomicRanges-method	GenomicRanges-comparison
duplicated,SummarizedExperiment-method	SummarizedExperiment-class
duplicated.GenomicRanges	GenomicRanges-comparison
elementMetadata,GAlignmentsList-method	GAlignmentsList-class
elementMetadata,GIntervalTree-method	GIntervalTree-class
elementMetadata,GRangesList-method	GRangesList-class
elementMetadata,SummarizedExperiment-method	SummarizedExperiment-class
elementMetadata<-,GAlignmentPairs-method	GAlignmentPairs-class
elementMetadata<-,GAlignments-method	GAlignments-class
elementMetadata<-,GAlignmentsList-method	GAlignmentsList-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,GAlignments-method	GAlignments-class
end,GAlignmentsList-method	GAlignmentsList-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
explodeCigarOpLengths	cigar-utils
explodeCigarOps	cigar-utils
exptData	SummarizedExperiment-class
exptData,SummarizedExperiment-method	SummarizedExperiment-class
exptData<-	SummarizedExperiment-class
exptData<-,SummarizedExperiment,list-method	SummarizedExperiment-class
exptData<-,SummarizedExperiment,SimpleList-method	SummarizedExperiment-class
extractAlignmentRangesOnReference	cigar-utils
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,GAlignmentPairs,GRangesList-method	encodeOverlaps-methods
findCompatibleOverlaps,GAlignments,GRangesList-method	encodeOverlaps-methods
findMatches,GAlignmentPairs,Vector-method	findOverlaps-methods
findMatches,GAlignments,GAlignments-method	findOverlaps-methods
findMatches,GAlignments,Vector-method	findOverlaps-methods
findMatches,GAlignmentsList,GAlignmentsList-method	findOverlaps-methods
findMatches,GAlignmentsList,Vector-method	findOverlaps-methods
findMatches,GenomicRanges,GenomicRanges-method	GenomicRanges-comparison
findMatches,GenomicRanges,GRangesList-method	findOverlaps-methods
findMatches,GenomicRanges,RangedData-method	findOverlaps-methods
findMatches,GenomicRanges,RangesList-method	findOverlaps-methods
findMatches,GRangesList,GenomicRanges-method	findOverlaps-methods
findMatches,GRangesList,GRangesList-method	findOverlaps-methods
findMatches,GRangesList,RangedData-method	findOverlaps-methods
findMatches,GRangesList,RangesList-method	findOverlaps-methods
findMatches,RangedData,GenomicRanges-method	findOverlaps-methods
findMatches,RangedData,GRangesList-method	findOverlaps-methods
findMatches,RangesList,GenomicRanges-method	findOverlaps-methods
findMatches,RangesList,GRangesList-method	findOverlaps-methods
findMatches,Vector,GAlignmentPairs-method	findOverlaps-methods
findMatches,Vector,GAlignments-method	findOverlaps-methods
findMatches,Vector,GAlignmentsList-method	findOverlaps-methods
findOverlaps,GAlignmentPairs,GAlignmentPairs-method	findOverlaps-methods
findOverlaps,GAlignmentPairs,Vector-method	findOverlaps-methods
findOverlaps,GAlignments,GAlignments-method	findOverlaps-methods
findOverlaps,GAlignments,GRangesList-method	findOverlaps-methods
findOverlaps,GAlignments,Vector-method	findOverlaps-methods
findOverlaps,GAlignmentsList,GAlignmentsList-method	findOverlaps-methods
findOverlaps,GAlignmentsList,Vector-method	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,GAlignments-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,GAlignmentPairs-method	findOverlaps-methods
findOverlaps,Vector,GAlignments-method	findOverlaps-methods
findOverlaps,Vector,GAlignmentsList-method	findOverlaps-methods
findOverlaps,Vector,SummarizedExperiment-method	SummarizedExperiment-class
findOverlaps-methods	findOverlaps-methods
findSpliceOverlaps	findSpliceOverlaps-methods
findSpliceOverlaps,GAlignmentPairs,GRangesList-method	findSpliceOverlaps-methods
findSpliceOverlaps,GAlignments,GRangesList-method	findSpliceOverlaps-methods
findSpliceOverlaps,GRangesList,GRangesList-method	findSpliceOverlaps-methods
findSpliceOverlaps-methods	findSpliceOverlaps-methods
first	GAlignmentPairs-class
first,GAlignmentPairs-method	GAlignmentPairs-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
GAlignmentPairs	GAlignmentPairs-class
GAlignmentPairs-class	GAlignmentPairs-class
GAlignments	GAlignments-class
GAlignments-class	GAlignments-class
GAlignmentsList	GAlignmentsList-class
GAlignmentsList-class	GAlignmentsList-class
GappedAlignmentPairs	GAlignmentPairs-class
GappedAlignmentPairs-class	GAlignmentPairs-class
GappedAlignments	GAlignments-class
GappedAlignments-class	GAlignments-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
GIntervalTree	GIntervalTree-class
GIntervalTree-class	GIntervalTree-class
GRanges	GRanges-class
granges	GAlignments-class
granges,GAlignmentPairs-method	GAlignmentPairs-class
granges,GAlignments-method	GAlignments-class
granges,GAlignmentsList-method	GAlignmentsList-class
granges,RangesMapping-method	map-methods
granges,SummarizedExperiment-method	SummarizedExperiment-class
GRanges-class	GRanges-class
GRangesList	GRangesList-class
GRangesList-class	GRangesList-class
grglist	GAlignments-class
grglist,GAlignmentPairs-method	GAlignmentPairs-class
grglist,GAlignments-method	GAlignments-class
grglist,GAlignmentsList-method	GAlignmentsList-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	GAlignments-class
introns,GAlignmentPairs-method	GAlignmentPairs-class
introns,GAlignments-method	GAlignments-class
introns,GAlignmentsList-method	GAlignmentsList-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	GAlignmentPairs-class
isProperPair,GAlignmentPairs-method	GAlignmentPairs-class
keepSeqlevels	seqlevels-utils
last	GAlignmentPairs-class
last,GAlignmentPairs-method	GAlignmentPairs-class
left	GAlignmentPairs-class
left,GAlignmentPairs-method	GAlignmentPairs-class
length,GAlignmentPairs-method	GAlignmentPairs-class
length,GAlignments-method	GAlignments-class
length,GenomicRanges-method	GRanges-class
length,Seqinfo-method	Seqinfo-class
makeGAlignmentsListFromFeatureFragments	GAlignmentsList-class
makeGRangesFromDataFrame	makeGRangesFromDataFrame
makeGRangesListFromFeatureFragments	GRangesList-class
makeSeqnameIds	makeSeqnameIds
map,GenomicRanges,GAlignments-method	map-methods
map,GenomicRanges,GRangesList-method	map-methods
match,GAlignmentPairs,Vector-method	findOverlaps-methods
match,GAlignments,GAlignments-method	findOverlaps-methods
match,GAlignments,Vector-method	findOverlaps-methods
match,GAlignmentsList,GAlignmentsList-method	findOverlaps-methods
match,GAlignmentsList,Vector-method	findOverlaps-methods
match,GenomicRanges,GenomicRanges-method	GenomicRanges-comparison
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,SummarizedExperiment-method	SummarizedExperiment-class
match,SummarizedExperiment,Vector-method	SummarizedExperiment-class
match,Vector,GAlignmentPairs-method	findOverlaps-methods
match,Vector,GAlignments-method	findOverlaps-methods
match,Vector,GAlignmentsList-method	findOverlaps-methods
match,Vector,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,GAlignmentPairs-method	GAlignmentPairs-class
names,GAlignments-method	GAlignments-class
names,GAlignmentsList-method	GAlignmentsList-class
names,GenomicRanges-method	GRanges-class
names,GIntervalTree-method	GIntervalTree-class
names,Seqinfo-method	Seqinfo-class
names<-,GAlignmentPairs-method	GAlignmentPairs-class
names<-,GAlignments-method	GAlignments-class
names<-,GAlignmentsList-method	GAlignmentsList-class
names<-,GenomicRanges-method	GRanges-class
names<-,Seqinfo-method	Seqinfo-class
narrow,GAlignments-method	intra-range-methods
narrow,GAlignmentsList-method	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
ngap,GAlignmentPairs-method	GAlignmentPairs-class
ngap,GAlignments-method	GAlignments-class
ngap,GAlignmentsList-method	GAlignmentsList-class
Ops,GenomicRanges,numeric-method	intra-range-methods
order,GenomicRanges-method	GenomicRanges-comparison
order,SummarizedExperiment-method	SummarizedExperiment-class
overlapsAny,GAlignmentPairs,Vector-method	findOverlaps-methods
overlapsAny,GAlignments,GAlignments-method	findOverlaps-methods
overlapsAny,GAlignments,Vector-method	findOverlaps-methods
overlapsAny,GAlignmentsList,GAlignmentsList-method	findOverlaps-methods
overlapsAny,GAlignmentsList,Vector-method	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,GAlignmentPairs-method	findOverlaps-methods
overlapsAny,Vector,GAlignments-method	findOverlaps-methods
overlapsAny,Vector,GAlignmentsList-method	findOverlaps-methods
overlapsAny,Vector,SummarizedExperiment-method	SummarizedExperiment-class
pgap,GRanges,GRanges-method	setops-methods
phicoef	phicoef
pintersect,GAlignments,GRanges-method	setops-methods
pintersect,GRanges,GAlignments-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
promoters,GenomicRanges-method	intra-range-methods
promoters,GRangesList-method	GRangesList-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	GAlignments-class
qnarrow,GAlignments-method	GAlignments-class
qnarrow,GAlignmentsList-method	GAlignmentsList-class
queryLoc2refLoc	cigar-utils
queryLocs2refLocs	cigar-utils
qwidth	GAlignments-class
qwidth,GAlignments-method	GAlignments-class
qwidth,GAlignmentsList-method	GAlignmentsList-class
range,GenomicRanges-method	inter-range-methods
range,GRangesList-method	GRangesList-class
ranges,GAlignments-method	GAlignments-class
ranges,GAlignmentsList-method	GAlignmentsList-class
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
readGAlignmentPairs	GAlignmentPairs-class
readGAlignments	GAlignments-class
readGAlignmentsList	GAlignmentsList-class
readGappedAlignmentPairs	GAlignmentPairs-class
readGappedAlignments	GAlignments-class
reduce,GenomicRanges-method	inter-range-methods
reduce,GRangesList-method	GRangesList-class
renameSeqlevels	seqlevels-utils
resize,GenomicRanges-method	intra-range-methods
resize,SummarizedExperiment-method	SummarizedExperiment-class
restoreSeqlevels	seqlevels-utils
restrict,GenomicRanges-method	intra-range-methods
restrict,GRangesList-method	GRangesList-class
restrict,SummarizedExperiment-method	SummarizedExperiment-class
rglist	GAlignments-class
rglist,GAlignments-method	GAlignments-class
rglist,GAlignmentsList-method	GAlignmentsList-class
right	GAlignmentPairs-class
right,GAlignmentPairs-method	GAlignmentPairs-class
rname	GAlignments-class
rname,GAlignments-method	GAlignments-class
rname,GAlignmentsList-method	GAlignmentsList-class
rname<-	GAlignments-class
rname<-,GAlignments-method	GAlignments-class
rname<-,GAlignmentsList-method	GAlignmentsList-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,GIntervalTree-method	GIntervalTree-class
score,GRangesList-method	GRangesList-class
selectEncodingWithCompatibleStrand	encodeOverlaps-methods
Seqinfo	Seqinfo-class
seqinfo	seqinfo
seqinfo,GAlignmentPairs-method	GAlignmentPairs-class
seqinfo,GAlignments-method	GAlignments-class
seqinfo,GAlignmentsList-method	GAlignmentsList-class
seqinfo,GIntervalTree-method	GIntervalTree-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<-,GAlignmentPairs-method	GAlignmentPairs-class
seqinfo<-,GAlignments-method	GAlignments-class
seqinfo<-,GAlignmentsList-method	GAlignmentsList-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-utils	seqlevels-utils
seqlevels0	seqinfo
seqlevels<-	seqinfo
seqlevels<-,ANY-method	seqinfo
seqlevels<-,Seqinfo-method	Seqinfo-class
seqlevelsInUse	seqinfo
seqlevelsInUse,CompressedList-method	seqinfo
seqlevelsInUse,GAlignmentPairs-method	GAlignmentPairs-class
seqlevelsInUse,SummarizedExperiment-method	SummarizedExperiment-class
seqlevelsInUse,Vector-method	seqinfo
seqnames	seqinfo
seqnames,GAlignmentPairs-method	GAlignmentPairs-class
seqnames,GAlignments-method	GAlignments-class
seqnames,GAlignmentsList-method	GAlignmentsList-class
seqnames,GIntervalTree-method	GIntervalTree-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<-,GAlignments-method	GAlignments-class
seqnames<-,GAlignmentsList-method	GAlignmentsList-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
seqnameStyle<-,Seqinfo-method	Seqinfo-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,GAlignmentPairs-method	GAlignmentPairs-class
show,GAlignments-method	GAlignments-class
show,GAlignmentsList-method	GAlignmentsList-class
show,GappedAlignmentPairs-method	GAlignmentPairs-class
show,GappedAlignments-method	GAlignments-class
show,GenomicRanges-method	GRanges-class
show,GIntervalTree-method	GIntervalTree-class
show,GRangesList-method	GRangesList-class
show,Seqinfo-method	Seqinfo-class
show,SummarizedExperiment-method	SummarizedExperiment-class
SimpleGenomicRangesList-class	GenomicRangesList-class
sort,SummarizedExperiment-method	SummarizedExperiment-class
sortSeqlevels	seqinfo
sortSeqlevels,ANY-method	seqinfo
sortSeqlevels,character-method	seqinfo
split,SummarizedExperiment,ANY-method	SummarizedExperiment-class
split,SummarizedExperiment-method	SummarizedExperiment-class
splitAsListReturnedClass,GAlignments-method	GAlignments-class
splitAsListReturnedClass,GRange	GRanges-class
splitAsListReturnedClass,GRanges-method	GRanges-class
splitAsListReturnedClass,SummarizedExperiment-method	SummarizedExperiment-class
splitCigar	cigar-utils
start,GAlignments-method	GAlignments-class
start,GAlignmentsList-method	GAlignmentsList-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,GAlignmentPairs-method	GAlignmentPairs-class
strand,GAlignments-method	GAlignments-class
strand,GAlignmentsList-method	GAlignmentsList-class
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,Rle-method	strand-utils
strand,SummarizedExperiment-method	SummarizedExperiment-class
strand-utils	strand-utils
strand<-,DataTable-method	strand-utils
strand<-,GAlignmentPairs-method	GAlignmentPairs-class
strand<-,GAlignments-method	GAlignments-class
strand<-,GAlignmentsList-method	GAlignmentsList-class
strand<-,GenomicRanges-method	GRanges-class
strand<-,GRangesList-method	GRangesList-class
strand<-,SummarizedExperiment-method	SummarizedExperiment-class
subsetByOverlaps,GAlignmentPairs,Vector-method	findOverlaps-methods
subsetByOverlaps,GAlignments,GAlignments-method	findOverlaps-methods
subsetByOverlaps,GAlignments,Vector-method	findOverlaps-methods
subsetByOverlaps,GAlignmentsList,GAlignmentsList-method	findOverlaps-methods
subsetByOverlaps,GAlignmentsList,Vector-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
subsetByOverlaps,SummarizedExperiment,SummarizedExperiment-method	SummarizedExperiment-class
subsetByOverlaps,SummarizedExperiment,Vector-method	SummarizedExperiment-class
subsetByOverlaps,Vector,GAlignmentPairs-method	findOverlaps-methods
subsetByOverlaps,Vector,GAlignments-method	findOverlaps-methods
subsetByOverlaps,Vector,GAlignmentsList-method	findOverlaps-methods
subsetByOverlaps,Vector,SummarizedExperiment-method	SummarizedExperiment-class
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,GAlignmentPairs-method	summarizeOverlaps
summarizeOverlaps,GRanges,GAlignments-method	summarizeOverlaps
summarizeOverlaps,GRanges,GAlignmentsList-method	summarizeOverlaps
summarizeOverlaps,GRangesList,GAlignmentPairs-method	summarizeOverlaps
summarizeOverlaps,GRangesList,GAlignments-method	summarizeOverlaps
summarizeOverlaps,GRangesList,GAlignmentsList-method	summarizeOverlaps
tileGenome	tileGenome
trim,GenomicRanges-method	intra-range-methods
Union	summarizeOverlaps
union,GRanges,GRanges-method	setops-methods
unlist,GAlignmentPairs-method	GAlignmentPairs-class
updateObject,GAlignments-method	GAlignments-class
updateObject,GAlignmentsList-method	GAlignmentsList-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,GAlignments-method	GAlignments-class
width,GAlignmentsList-method	GAlignmentsList-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-method	GRanges-class
[,GIntervalTree-method	GIntervalTree-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
[[,GAlignmentPairs,ANY,ANY-method	GAlignmentPairs-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