$,GenomicRanges-method	GRanges-class
$<-,GenomicRanges-method	GRanges-class
absoluteRanges	absoluteRanges
as.character,GenomicRanges-method	GRanges-class
as.data.frame,GenomicRanges-method	GRanges-class
as.data.frame,GPos-method	GPos-class
as.data.frame.GPos	GPos-class
as.factor,GenomicRanges-method	GRanges-class
bindAsGRanges	genomicvars
bindROWS,GenomicRanges-method	GRanges-class
binnedAverage	genomicvars
checkConstraint	constraint
class:CompressedGenomicRangesList	GenomicRangesList-class
class:CompressedGRangesList	GRangesList-class
class:Constraint	constraint
class:Constraint_OR_NULL	constraint
class:DelegatingGenomicRanges	DelegatingGenomicRanges-class
class:GenomicPos	GRanges-class
class:GenomicRanges	GRanges-class
class:GenomicRangesList	GenomicRangesList-class
class:GenomicRanges_OR_GenomicRangesList	GenomicRangesList-class
class:GenomicRanges_OR_GRangesList	GRangesList-class
class:GNCList	GNCList-class
class:GPos	GPos-class
class:GRanges	GRanges-class
class:GRangesFactor	GRangesFactor-class
class:GRangesList	GRangesList-class
class:IRanges_OR_IPos	GRanges-class
class:SimpleGenomicRangesList	GenomicRangesList-class
class:SimpleGRangesList	GRangesList-class
class:StitchedGPos	GPos-class
class:UnstitchedGPos	GPos-class
coerce,ANY,GenomicRanges-method	GRanges-class
coerce,ANY,GPos-method	GPos-class
coerce,ANY,GRangesFactor-method	GRangesFactor-class
coerce,ANY,StitchedGPos-method	GPos-class
coerce,ANY,UnstitchedGPos-method	GPos-class
coerce,character,GRanges-method	GRanges-class
coerce,CompressedGRangesList,CompressedIRangesList-method	GRangesList-class
coerce,CompressedGRangesList,IntegerRangesList-method	GRangesList-class
coerce,CompressedGRangesList,IRangesList-method	GRangesList-class
coerce,data.frame,GRanges-method	makeGRangesFromDataFrame
coerce,DataFrame,GRanges-method	makeGRangesFromDataFrame
coerce,Factor,GRanges-method	GRangesFactor-class
coerce,factor,GRanges-method	GRanges-class
coerce,GenomicRanges,CompressedIRangesList-method	GRanges-class
coerce,GenomicRanges,GNCList-method	GNCList-class
coerce,GenomicRanges,GRanges-method	GRanges-class
coerce,GenomicRanges,Grouping-method	GRanges-class
coerce,GenomicRanges,IntegerRangesList-method	GRanges-class
coerce,GenomicRanges,IRangesList-method	GRanges-class
coerce,GenomicRangesList,SimpleGRangesList-method	GRangesList-class
coerce,GNCList,GRanges-method	GNCList-class
coerce,GRanges,GPos-method	GPos-class
coerce,GRanges,StitchedGPos-method	GPos-class
coerce,GRanges,UnstitchedGPos-method	GPos-class
coerce,IntegerRangesList,GRanges-method	GRanges-class
coerce,List,CompressedGRangesList-method	GRangesList-class
coerce,list,CompressedGRangesList-method	GRangesList-class
coerce,List,GRangesList-method	GRangesList-class
coerce,list,GRangesList-method	GRangesList-class
coerce,List,SimpleGRangesList-method	GRangesList-class
coerce,list,SimpleGRangesList-method	GRangesList-class
coerce,RleList,GRanges-method	genomicvars
coerce,RleViewsList,GRanges-method	genomicvars
coerce,Seqinfo,GRanges-method	GRanges-class
coerce,Seqinfo,IntegerRangesList-method	GRanges-class
coerce,SimpleGenomicRangesList,SimpleGRangesList-method	GRangesList-class
coerce,SimpleList,SimpleGRangesList-method	GRangesList-class
coerce,StitchedGPos,GRanges-method	GPos-class
coerce,UnstitchedGPos,GRanges-method	GPos-class
CompressedGenomicRangesList	GenomicRangesList-class
CompressedGenomicRangesList-class	GenomicRangesList-class
CompressedGRangesList	GRangesList-class
CompressedGRangesList-class	GRangesList-class
Constraint	constraint
constraint	constraint
Constraint-class	constraint
constraint<-	constraint
Constraints	constraint
Constraint_OR_NULL	constraint
Constraint_OR_NULL-class	constraint
countOverlaps	findOverlaps-methods
countOverlaps,GenomicRanges,GenomicRanges-method	findOverlaps-methods
coverage	coverage-methods
coverage,GenomicRanges-method	coverage-methods
coverage,GRangesList-method	coverage-methods
coverage,StitchedGPos-method	coverage-methods
coverage-methods	coverage-methods
DelegatingGenomicRanges-class	DelegatingGenomicRanges-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
distance	nearest-methods
distance,GenomicRanges,GenomicRanges-method	nearest-methods
distanceToNearest	nearest-methods
distanceToNearest,GenomicRanges,GenomicRanges-method	nearest-methods
distanceToNearest,GenomicRanges,missing-method	nearest-methods
duplicated,GenomicRanges-method	GenomicRanges-comparison
duplicated.GenomicRanges	GenomicRanges-comparison
elementMetadata,GenomicRangesList-method	GenomicRangesList-class
elementMetadata<-,CompressedGenomicRangesList-method	GenomicRangesList-class
end,GNCList-method	GNCList-class
end,GRangesFactor-method	GRangesFactor-class
end<-,CompressedGenomicRangesList-method	GenomicRangesList-class
end<-,GenomicRanges-method	GRanges-class
extractROWS,GenomicRangesList,ANY-method	GenomicRangesList-class
FactorToClass,GRanges-method	GRangesFactor-class
findOverlaps	findOverlaps-methods
findOverlaps,GenomicRanges,GenomicRanges-method	findOverlaps-methods
findOverlaps,GenomicRanges,GRangesList-method	findOverlaps-methods
findOverlaps,GRangesList,GenomicRanges-method	findOverlaps-methods
findOverlaps,GRangesList,GRangesList-method	findOverlaps-methods
findOverlaps-methods	findOverlaps-methods
flank	intra-range-methods
flank,GenomicRanges-method	intra-range-methods
follow	nearest-methods
follow,GenomicRanges,GenomicRanges-method	nearest-methods
follow,GenomicRanges,missing-method	nearest-methods
from_GPos_to_GRanges	GPos-class
gaps	inter-range-methods
gaps,GenomicRanges-method	inter-range-methods
genomic-range-squeezers	genomic-range-squeezers
GenomicPos	GRanges-class
GenomicPos-class	GRanges-class
GenomicRanges	GRanges-class
GenomicRanges-class	GRanges-class
GenomicRanges-comparison	GenomicRanges-comparison
GenomicRangesList	GenomicRangesList-class
GenomicRangesList-class	GenomicRangesList-class
GenomicRanges_OR_GenomicRangesList	GenomicRangesList-class
GenomicRanges_OR_GenomicRangesList-class	GenomicRangesList-class
GenomicRanges_OR_GRangesList	GRangesList-class
GenomicRanges_OR_GRangesList-class	GRangesList-class
GenomicRanges_OR_missing-class	GRanges-class
genomicvariables	genomicvars
genomicvars	genomicvars
getListElement,GenomicRanges-method	GRanges-class
getListElement,GenomicRangesList-method	GenomicRangesList-class
GNCList	GNCList-class
GNCList-class	GNCList-class
GPos	GPos-class
GPos-class	GPos-class
GRanges	GRanges-class
granges	genomic-range-squeezers
granges,GenomicRanges-method	GRanges-class
granges,GNCList-method	GNCList-class
granges,GRangesFactor-method	GRangesFactor-class
GRanges-class	GRanges-class
GRangesFactor	GRangesFactor-class
GRangesFactor-class	GRangesFactor-class
GRangesList	GRangesList-class
GRangesList-class	GRangesList-class
grglist	genomic-range-squeezers
grglist,Pairs-method	genomic-range-squeezers
inter-range-methods	inter-range-methods
intersect	setops-methods
intersect,GenomicRanges,GenomicRanges-method	setops-methods
intersect,GenomicRanges,Vector-method	setops-methods
intersect,GRangesList,GRangesList-method	setops-methods
intersect,Vector,GenomicRanges-method	setops-methods
intra-range-methods	intra-range-methods
invertStrand,character-method	strand-utils
invertStrand,factor-method	strand-utils
invertStrand,integer-method	strand-utils
invertStrand,logical-method	strand-utils
invertStrand,NULL-method	strand-utils
invertStrand,Rle-method	strand-utils
invertStrand,RleList-method	strand-utils
IRanges_OR_IPos	GRanges-class
IRanges_OR_IPos-class	GRanges-class
is.unsorted,GenomicRanges-method	GenomicRanges-comparison
isDisjoint	inter-range-methods
isDisjoint,GenomicRanges-method	inter-range-methods
isDisjoint,GRangesList-method	inter-range-methods
isDisjoint,StitchedGPos-method	inter-range-methods
isSmallGenome	absoluteRanges
length,GenomicRanges-method	GRanges-class
length,GenomicRangesList-method	GenomicRangesList-class
length,GNCList-method	GNCList-class
makeGRangesFromDataFrame	makeGRangesFromDataFrame
makeGRangesListFromDataFrame	makeGRangesListFromDataFrame
makeGRangesListFromFeatureFragments	GRangesList-class
match,GenomicRanges,GenomicRanges-method	GenomicRanges-comparison
mcolAsRleList	genomicvars
names,GenomicRanges-method	GRanges-class
names,GenomicRangesList-method	GenomicRangesList-class
names,GNCList-method	GNCList-class
names<-,GenomicRanges-method	GRanges-class
names<-,GenomicRangesList-method	GenomicRangesList-class
narrow	intra-range-methods
narrow,GenomicRanges-method	intra-range-methods
nearest	nearest-methods
nearest,GenomicRanges,GenomicRanges-method	nearest-methods
nearest,GenomicRanges,missing-method	nearest-methods
nearest-methods	nearest-methods
nearestKNeighbors	nearest-methods
nearestKNeighbors,GenomicRanges,GenomicRanges-method	nearest-methods
nearestKNeighbors,GenomicRanges,missing-method	nearest-methods
order,GenomicRanges-method	GenomicRanges-comparison
overlapsAny	findOverlaps-methods
parallel_slot_names,GRanges-method	GRanges-class
pcompare	GenomicRanges-comparison
pcompare,GenomicRanges,GenomicRanges-method	GenomicRanges-comparison
pgap	setops-methods
pgap,GRanges,GRanges-method	setops-methods
phicoef	phicoef
pintersect	setops-methods
pintersect,GRanges,GRanges-method	setops-methods
pintersect,GRanges,GRangesList-method	setops-methods
pintersect,GRangesList,GRanges-method	setops-methods
pos,GPos-method	GPos-class
pos,GRangesFactor-method	GRangesFactor-class
precede	nearest-methods
precede,GenomicRanges,GenomicRanges-method	nearest-methods
precede,GenomicRanges,missing-method	nearest-methods
promoters	intra-range-methods
promoters,GenomicRanges-method	intra-range-methods
psetdiff	setops-methods
psetdiff,GRanges,GRanges-method	setops-methods
psetdiff,GRanges,GRangesList-method	setops-methods
punion	setops-methods
punion,GRanges,GRanges-method	setops-methods
punion,GRanges,GRangesList-method	setops-methods
punion,GRangesList,GRanges-method	setops-methods
range	inter-range-methods
range,GenomicRanges-method	inter-range-methods
range,GRangesList-method	inter-range-methods
range,StitchedGPos-method	inter-range-methods
ranges,CompressedGRangesList-method	GRangesList-class
ranges,DelegatingGenomicRanges-method	DelegatingGenomicRanges-class
ranges,GNCList-method	GNCList-class
ranges,GRanges-method	GRanges-class
ranges,GRangesFactor-method	GRangesFactor-class
ranges<-,CompressedGRangesList-method	GRangesList-class
ranges<-,GenomicRanges-method	GRanges-class
rank,GenomicRanges-method	GenomicRanges-comparison
reduce	inter-range-methods
reduce,GenomicRanges-method	inter-range-methods
reduce,GRangesList-method	inter-range-methods
relativeRanges	absoluteRanges
relistToClass,GRanges-method	GRangesList-class
resize	intra-range-methods
resize,GenomicRanges-method	intra-range-methods
restrict	intra-range-methods
restrict,GenomicRanges-method	intra-range-methods
score,GenomicRanges-method	GRanges-class
score,GenomicRangesList-method	GenomicRangesList-class
score<-,GenomicRanges-method	GRanges-class
score<-,GenomicRangesList-method	GenomicRangesList-class
selfmatch,GenomicRanges-method	GenomicRanges-comparison
seqinfo,CompressedGenomicRangesList-method	GenomicRangesList-class
seqinfo,DelegatingGenomicRanges-method	DelegatingGenomicRanges-class
seqinfo,GenomicRangesList-method	GenomicRangesList-class
seqinfo,GNCList-method	GNCList-class
seqinfo,GRanges-method	GRanges-class
seqinfo,GRangesFactor-method	GRangesFactor-class
seqinfo,List-method	GRanges-class
seqinfo<-,CompressedGenomicRangesList-method	GenomicRangesList-class
seqinfo<-,GenomicRanges-method	GRanges-class
seqinfo<-,List-method	GRanges-class
seqnames,DelegatingGenomicRanges-method	DelegatingGenomicRanges-class
seqnames,GenomicRangesList-method	GenomicRangesList-class
seqnames,GNCList-method	GNCList-class
seqnames,GRanges-method	GRanges-class
seqnames,GRangesFactor-method	GRangesFactor-class
seqnames<-,CompressedGenomicRangesList-method	GenomicRangesList-class
seqnames<-,GenomicRanges-method	GRanges-class
setdiff	setops-methods
setdiff,GenomicRanges,GenomicRanges-method	setops-methods
setdiff,GenomicRanges,Vector-method	setops-methods
setdiff,GRangesList,GRangesList-method	setops-methods
setdiff,Vector,GenomicRanges-method	setops-methods
setops-methods	setops-methods
shift	intra-range-methods
shift,GenomicRanges-method	intra-range-methods
show,GenomicRanges-method	GRanges-class
show,GenomicRangesList-method	GenomicRangesList-class
show,GPos-method	GPos-class
show,GRangesFactor-method	GRangesFactor-class
SimpleGenomicRangesList	GenomicRangesList-class
SimpleGenomicRangesList-class	GenomicRangesList-class
SimpleGRangesList	GRangesList-class
SimpleGRangesList-class	GRangesList-class
slidingWindows	tile-methods
slidingWindows,GenomicRanges-method	tile-methods
sort,CompressedGRangesList-method	GRangesList-class
sort,GenomicRanges-method	GenomicRanges-comparison
sort,GRangesList-method	GRangesList-class
sort.GenomicRanges	GenomicRanges-comparison
sort.GRangesList	GRangesList-class
start,GenomicRanges-method	GRanges-class
start,GNCList-method	GNCList-class
start,GRangesFactor-method	GRangesFactor-class
start<-,CompressedGenomicRangesList-method	GenomicRangesList-class
start<-,GenomicRanges-method	GRanges-class
StitchedGPos	GPos-class
StitchedGPos-class	GPos-class
strand,character-method	strand-utils
strand,DataFrame-method	strand-utils
strand,DelegatingGenomicRanges-method	DelegatingGenomicRanges-class
strand,factor-method	strand-utils
strand,GenomicRangesList-method	GenomicRangesList-class
strand,GNCList-method	GNCList-class
strand,GRanges-method	GRanges-class
strand,GRangesFactor-method	GRangesFactor-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,RleList-method	strand-utils
strand-utils	strand-utils
strand<-,CompressedGenomicRangesList,ANY-method	GenomicRangesList-class
strand<-,CompressedGenomicRangesList,character-method	GenomicRangesList-class
strand<-,DataFrame,ANY-method	strand-utils
strand<-,GenomicRanges,ANY-method	GRanges-class
subsetByOverlaps	findOverlaps-methods
subtract	subtract-methods
subtract,GenomicRanges,GenomicRanges-method	subtract-methods
subtract-methods	subtract-methods
summary,GenomicRanges-method	GRanges-class
summary,GPos-method	GPos-class
summary.GenomicRanges	GRanges-class
summary.GPos	GPos-class
terminators	intra-range-methods
terminators,GenomicRanges-method	intra-range-methods
tile	tile-methods
tile,GenomicRanges-method	tile-methods
tile-methods	tile-methods
tileGenome	tileGenome
trim	intra-range-methods
trim,GenomicRanges-method	intra-range-methods
trim,GRangesList-method	intra-range-methods
union	setops-methods
union,GenomicRanges,GenomicRanges-method	setops-methods
union,GenomicRanges,Vector-method	setops-methods
union,GRangesList,GRangesList-method	setops-methods
union,Vector,GenomicRanges-method	setops-methods
unlist,GenomicRangesList-method	GenomicRangesList-class
UnstitchedGPos	GPos-class
UnstitchedGPos-class	GPos-class
update,DelegatingGenomicRanges-method	DelegatingGenomicRanges-class
update,GRanges-method	GRanges-class
updateObject,GenomicRangesList-method	GenomicRangesList-class
updateObject,GPos-method	GPos-class
updateObject,GRanges-method	GRanges-class
update_ranges,GenomicRanges-method	intra-range-methods
width,GenomicRanges-method	GRanges-class
width,GNCList-method	GNCList-class
width,GRangesFactor-method	GRangesFactor-class
width<-,CompressedGenomicRangesList-method	GenomicRangesList-class
width<-,GenomicRanges-method	GRanges-class
[,CompressedGRangesList,ANY-method	GRangesList-class
[,list_OR_List,GenomicRanges-method	GRanges-class
[<-,CompressedGRangesList,ANY,ANY,ANY-method	GRangesList-class
[<-,CompressedGRangesList,ANY-method	GRangesList-class
[<-,CompressedGRangesList-method	GRangesList-class
