!,Rle-method	Rle-utils
!=,ANY,Vector-method	Vector-comparison
!=,Vector,ANY-method	Vector-comparison
!=,Vector,Vector-method	Vector-comparison
$,List-method	List-class
$<-,List-method	List-class
%in%,ANY,Vector-method	Vector-comparison
%in%,Rle,ANY-method	Rle-class
%in%,Vector,ANY-method	Vector-comparison
%in%,Vector,Vector-method	Vector-comparison
&,FilterRules,FilterRules-method	FilterRules-class
.Call2	S4Vectors-internals
<,ANY,Vector-method	Vector-comparison
<,Vector,ANY-method	Vector-comparison
<,Vector,Vector-method	Vector-comparison
<=,ANY,Vector-method	Vector-comparison
<=,DataFrame,DataFrame-method	DataFrame-comparison
<=,Vector,ANY-method	Vector-comparison
<=,Vector,Vector-method	Vector-comparison
==,ANY,Vector-method	Vector-comparison
==,DataFrame,DataFrame-method	DataFrame-comparison
==,Vector,ANY-method	Vector-comparison
==,Vector,Vector-method	Vector-comparison
>,ANY,Vector-method	Vector-comparison
>,Vector,ANY-method	Vector-comparison
>,Vector,Vector-method	Vector-comparison
>=,ANY,Vector-method	Vector-comparison
>=,Vector,ANY-method	Vector-comparison
>=,Vector,Vector-method	Vector-comparison
active	FilterRules-class
active,FilterRules-method	FilterRules-class
active<-	FilterRules-class
active<-,FilterRules-method	FilterRules-class
aggregate	aggregate-methods
aggregate,data.frame-method	aggregate-methods
aggregate,List-method	aggregate-methods
aggregate,matrix-method	aggregate-methods
aggregate,Rle-method	aggregate-methods
aggregate,ts-method	aggregate-methods
aggregate,Vector-method	aggregate-methods
aggregate-methods	aggregate-methods
aggregate.Vector	aggregate-methods
Annotated	Annotated-class
Annotated-class	Annotated-class
anyDuplicated,NSBS-method	subsetting-utils
anyDuplicated,RangeNSBS-method	subsetting-utils
anyDuplicated,Rle-method	Rle-class
anyDuplicated,RleNSBS-method	Rle-class
anyDuplicated,Vector-method	Vector-comparison
anyDuplicated.NSBS	subsetting-utils
anyDuplicated.Rle	Rle-class
anyDuplicated.Vector	Vector-comparison
anyNA,Rle-method	Rle-class
anyNA,Vector-method	Vector-class
append	Vector-class
append,Rle,vector-method	Rle-class
append,vector,Rle-method	Rle-class
append,Vector,Vector-method	Vector-class
as.character,Factor-method	Factor-class
as.character,LLint-method	LLint-class
as.character,Vector-method	Vector-class
as.character.LLint	LLint-class
as.complex,Vector-method	Vector-class
as.data.frame,DataFrame-method	DataFrame-class
as.data.frame,Hits-method	Hits-class
as.data.frame,List-method	List-class
as.data.frame,Pairs-method	Pairs-class
as.data.frame,Rle-method	Rle-class
as.data.frame,Vector-method	Vector-class
as.data.frame.Hits	Hits-class
as.data.frame.Vector	Vector-class
as.double,Vector-method	Vector-class
as.env	Vector-class
as.env,NULL-method	Vector-class
as.env,SimpleList-method	SimpleList-class
as.env,Vector-method	Vector-class
as.factor,Factor-method	Factor-class
as.factor,Rle-method	Rle-class
as.integer,Factor-method	Factor-class
as.integer,LLint-method	LLint-class
as.integer,NativeNSBS-method	subsetting-utils
as.integer,RangeNSBS-method	subsetting-utils
as.integer,RleNSBS-method	Rle-class
as.integer,Vector-method	Vector-class
as.integer.LLint	LLint-class
as.list,List-method	List-class
as.list,Rle-method	Rle-class
as.list,SimpleList-method	SimpleList-class
as.list,TransposedDataFrame-method	TransposedDataFrame-class
as.list,Vector-method	Vector-class
as.list.Vector	Vector-class
as.LLint	LLint-class
as.logical,LLint-method	LLint-class
as.logical,Vector-method	Vector-class
as.logical.LLint	LLint-class
as.matrix,DataFrame-method	DataFrame-class
as.matrix,Hits-method	Hits-class
as.matrix,HitsList-method	HitsList-class
as.matrix,TransposedDataFrame-method	TransposedDataFrame-class
as.matrix,Vector-method	Vector-class
as.matrix.Vector	Vector-class
as.numeric,LLint-method	LLint-class
as.numeric,Vector-method	Vector-class
as.numeric.LLint	LLint-class
as.raw,Vector-method	Vector-class
as.table,Hits-method	Hits-class
as.table,HitsList-method	HitsList-class
as.vector,Rle-method	Rle-class
as.vector.Rle	Rle-class
atomic	S4Vectors-internals
atomic-class	S4Vectors-internals
bindCOLS	bindROWS
bindCOLS,TransposedDataFrame-method	TransposedDataFrame-class
bindROWS	bindROWS
bindROWS,ANY-method	bindROWS
bindROWS,DataFrame-method	DataFrame-combine
bindROWS,Factor-method	Factor-class
bindROWS,Hits-method	Hits-class
bindROWS,LLint-method	LLint-class
bindROWS,NULL-method	bindROWS
bindROWS,Rle-method	Rle-class
bindROWS,TransposedDataFrame-method	TransposedDataFrame-class
bindROWS,Vector-method	Vector-class
breakTies	Hits-class
c	Vector-class
c,DataFrame-method	DataFrame-combine
c,LLint-method	LLint-class
c,Vector-method	Vector-class
cbind,DataFrame-method	DataFrame-combine
cbind,FilterMatrix-method	FilterMatrix-class
cbind,List-method	List-utils
cbind,RectangularData-method	RectangularData-class
cbind.DataFrame	DataFrame-combine
cbind.List	List-utils
cbind.RectangularData	RectangularData-class
cbind_mcols_for_display	show-utils
character_OR_NULL	S4Vectors-internals
character_OR_NULL-class	S4Vectors-internals
chartr,ANY,ANY,Rle-method	Rle-utils
class:atomic	S4Vectors-internals
class:character_OR_NULL	S4Vectors-internals
class:DataFrame	DataFrame-class
class:DataFrame_OR_NULL	S4Vectors-internals
class:DFrame	DataFrame-class
class:expression_OR_function	FilterRules-class
class:Factor	Factor-class
class:FilterRules	FilterRules-class
class:Hits	Hits-class
class:HitsList	HitsList-class
class:integer_OR_LLint	LLint-class
class:List	List-class
class:list_OR_List	List-class
class:LLint	LLint-class
class:NSBS	subsetting-utils
class:Pairs	Pairs-class
class:RectangularData	RectangularData-class
class:Rle	Rle-class
class:SelfHits	Hits-class
class:SelfHitsList	HitsList-class
class:SimpleList	SimpleList-class
class:SortedByQueryHits	Hits-class
class:SortedByQueryHitsList	HitsList-class
class:SortedByQuerySelfHits	Hits-class
class:SortedByQuerySelfHitsList	HitsList-class
class:TransposedDataFrame	TransposedDataFrame-class
class:Vector	Vector-class
class:vector_OR_factor	S4Vectors-internals
class:vector_OR_Vector	Vector-class
classNameForDisplay	show-utils
classNameForDisplay,ANY-method	show-utils
classNameForDisplay,AsIs-method	show-utils
classNameForDisplay,DFrame-method	DataFrame-class
classNameForDisplay,SimpleList-method	SimpleList-class
classNameForDisplay,SortedByQueryHits-method	Hits-class
coerce,ANY,AsIs-method	S4Vectors-internals
coerce,ANY,DataFrame-method	DataFrame-class
coerce,ANY,DFrame-method	DataFrame-class
coerce,ANY,FilterRules-method	FilterRules-class
coerce,ANY,List-method	List-class
coerce,ANY,Rle-method	Rle-class
coerce,ANY,SimpleList-method	SimpleList-class
coerce,ANY,vector-method	S4Vectors-internals
coerce,AsIs,DFrame-method	DataFrame-class
coerce,character,LLint-method	LLint-class
coerce,data.frame,DFrame-method	DataFrame-class
coerce,data.table,DFrame-method	DataFrame-class
coerce,DataFrame,TransposedDataFrame-method	TransposedDataFrame-class
coerce,DFrame,DataFrame-method	DataFrame-class
coerce,factor,Factor-method	Factor-class
coerce,function,FilterClosure-method	FilterRules-class
coerce,Hits,DFrame-method	Hits-class
coerce,Hits,SelfHits-method	Hits-class
coerce,Hits,SortedByQueryHits-method	Hits-class
coerce,Hits,SortedByQuerySelfHits-method	Hits-class
coerce,HitsList,SortedByQueryHitsList-method	HitsList-class
coerce,integer,List-method	List-class
coerce,integer,LLint-method	LLint-class
coerce,list,DFrame-method	DataFrame-class
coerce,List,list-method	List-class
coerce,list,List-method	SimpleList-class
coerce,list,TransposedDataFrame-method	TransposedDataFrame-class
coerce,list_OR_List,Pairs-method	Pairs-class
coerce,logical,LLint-method	LLint-class
coerce,NULL,DFrame-method	DataFrame-class
coerce,numeric,LLint-method	LLint-class
coerce,Pairs,DFrame-method	Pairs-class
coerce,Rle,character-method	Rle-class
coerce,Rle,complex-method	Rle-class
coerce,Rle,factor-method	Rle-class
coerce,Rle,integer-method	Rle-class
coerce,Rle,list-method	Rle-class
coerce,Rle,logical-method	Rle-class
coerce,Rle,numeric-method	Rle-class
coerce,Rle,raw-method	Rle-class
coerce,Rle,vector-method	Rle-class
coerce,SelfHits,SortedByQuerySelfHits-method	Hits-class
coerce,SimpleList,DataFrame-method	DataFrame-class
coerce,SimpleList,DFrame-method	DataFrame-class
coerce,SimpleList,FilterRules-method	FilterRules-class
coerce,SortedByQueryHits,SortedByQuerySelfHits-method	Hits-class
coerce,SortedByQueryHitsList,HitsList-method	HitsList-class
coerce,standardGeneric,FilterClosure-method	FilterRules-class
coerce,table,DFrame-method	DataFrame-class
coerce,TransposedDataFrame,DataFrame-method	TransposedDataFrame-class
coerce,Vector,character-method	Vector-class
coerce,Vector,complex-method	Vector-class
coerce,Vector,data.frame-method	Vector-class
coerce,Vector,DFrame-method	DataFrame-class
coerce,Vector,double-method	Vector-class
coerce,Vector,factor-method	Vector-class
coerce,Vector,integer-method	Vector-class
coerce,Vector,logical-method	Vector-class
coerce,Vector,numeric-method	Vector-class
coerce,Vector,raw-method	Vector-class
coerce,Vector,vector-method	Vector-class
coerce,vector_OR_Vector,Factor-method	Factor-class
coerce,xtabs,DFrame-method	DataFrame-class
colnames,DataFrame-method	DataFrame-class
colnames<-,DataFrame-method	DataFrame-class
combineCols	RectangularData-class
combineCols,DataFrame-method	DataFrame-combine
combineRows	RectangularData-class
combineRows,DataFrame-method	DataFrame-combine
combineUniqueCols	RectangularData-class
complete.cases,DataFrame-method	DataFrame-utils
Complex,Rle-method	Rle-utils
coolcat	show-utils
cor,Rle,Rle-method	Rle-utils
countLnodeHits	Hits-class
countLnodeHits,Hits-method	Hits-class
countMatches	Vector-comparison
countMatches,ANY,ANY-method	Vector-comparison
countQueryHits	Hits-class
countRnodeHits	Hits-class
countRnodeHits,Hits-method	Hits-class
countSubjectHits	Hits-class
cov,Rle,Rle-method	Rle-utils
DataFrame	DataFrame-class
DataFrame-class	DataFrame-class
DataFrame-combine	DataFrame-combine
DataFrame-utils	DataFrame-utils
DataFrame_OR_NULL	S4Vectors-internals
DataFrame_OR_NULL-class	S4Vectors-internals
decode	Rle-class
decode,ANY-method	Rle-class
decode,Rle-method	Rle-class
DFrame	DataFrame-class
DFrame-class	DataFrame-class
diff,Rle-method	Rle-utils
diff.Rle	Rle-utils
dim,DataFrame-method	DataFrame-class
dim,TransposedDataFrame-method	TransposedDataFrame-class
dimnames,DataFrame-method	DataFrame-class
dimnames,TransposedDataFrame-method	TransposedDataFrame-class
dimnames<-,DataFrame-method	DataFrame-class
dimnames<-,TransposedDataFrame-method	TransposedDataFrame-class
droplevels,List-method	List-utils
droplevels,Rle-method	Rle-utils
droplevels.List	List-utils
droplevels.Rle	Rle-utils
duplicated,DataFrame-method	DataFrame-comparison
duplicated,Rle-method	Rle-class
duplicated,Vector-method	Vector-comparison
duplicated.DataFrame	DataFrame-comparison
duplicated.Vector	Vector-comparison
duplicatedIntegerPairs	integer-utils
duplicatedIntegerQuads	integer-utils
elementMetadata	Vector-class
elementMetadata,Vector-method	Vector-class
elementMetadata<-	Vector-class
elementMetadata<-,Vector-method	Vector-class
elementNROWS	List-class
elementNROWS,ANY-method	List-class
elementNROWS,List-method	List-class
elementType	List-class
elementType,List-method	List-class
elementType,vector-method	List-class
end,Rle-method	Rle-class
endoapply	List-utils
eval,FilterRules,ANY-method	FilterRules-class
evalSeparately	FilterRules-class
evalSeparately,FilterRules-method	FilterRules-class
expand	expand-methods
expand,DataFrame-method	expand-methods
expand,Vector-method	expand-methods
expand.grid	Vector-class
expand.grid,Vector-method	Vector-class
expression_OR_function	FilterRules-class
expression_OR_function-class	FilterRules-class
extractCOLS	subsetting-utils
extractCOLS,TransposedDataFrame-method	TransposedDataFrame-class
extractROWS	subsetting-utils
extractROWS,ANY,ANY-method	subsetting-utils
extractROWS,array,RangeNSBS-method	subsetting-utils
extractROWS,data.frame,RangeNSBS-method	subsetting-utils
extractROWS,Rle,ANY-method	Rle-class
extractROWS,Rle,NSBS-method	Rle-class
extractROWS,Rle,RangeNSBS-method	Rle-class
extractROWS,Rle,RleNSBS-method	Rle-class
extractROWS,SortedByQueryHits,ANY-method	Hits-class
extractROWS,TransposedDataFrame,ANY-method	TransposedDataFrame-class
extractROWS,vector_OR_factor,RangeNSBS-method	subsetting-utils
Factor	Factor-class
Factor-class	Factor-class
FactorToClass	Factor-class
FactorToClass,vector_OR_Vector-method	Factor-class
Filter,List-method	List-utils
FilterMatrix	FilterMatrix-class
FilterMatrix-class	FilterMatrix-class
FilterRules	FilterRules-class
filterRules	FilterMatrix-class
filterRules,FilterMatrix-method	FilterMatrix-class
FilterRules-class	FilterRules-class
Find,List-method	List-utils
findMatches	Vector-comparison
findMatches,ANY,ANY-method	Vector-comparison
findMatches,ANY,missing-method	Vector-comparison
findRun	Rle-class
findRun,Rle-method	Rle-class
first	Pairs-class
first,Pairs-method	Pairs-class
first<-	Pairs-class
first<-,Pairs-method	Pairs-class
fold	S4Vectors-internals
from	Hits-class
from,Hits-method	Hits-class
getListElement	subsetting-utils
getListElement,List-method	List-class
getListElement,list-method	subsetting-utils
getListElement,TransposedDataFrame-method	TransposedDataFrame-class
get_showHeadLines	S4Vectors-internals
get_showTailLines	S4Vectors-internals
gsub,ANY,ANY,Rle-method	Rle-utils
head	Vector-class
head,RectangularData-method	RectangularData-class
head,Vector-method	Vector-class
head.RectangularData	RectangularData-class
head.Vector	Vector-class
Hits	Hits-class
Hits-class	Hits-class
Hits-comparison	Hits-comparison
Hits-setops	Hits-setops
HitsList	HitsList-class
HitsList-class	HitsList-class
horizontal_slot_names	RectangularData-class
horizontal_slot_names,DataFrame-method	DataFrame-class
integer_OR_LLint	LLint-class
integer_OR_LLint-class	LLint-class
intersect,ANY,Rle-method	Rle-class
intersect,Rle,ANY-method	Rle-class
intersect,Rle,Rle-method	Rle-class
intersect,Vector,Vector-method	Vector-setops
intersect.Vector	Vector-setops
IQR,Rle-method	Rle-utils
is.finite,Rle-method	Rle-class
is.LLint	LLint-class
is.na,DataFrame-method	DataFrame-utils
is.na,LLint-method	LLint-class
is.na,Rle-method	Rle-class
is.na,Vector-method	Vector-class
is.unsorted,Rle-method	Rle-class
isConstant	isSorted
isConstant,array-method	isSorted
isConstant,integer-method	isSorted
isConstant,numeric-method	isSorted
isEmpty	List-class
isEmpty,ANY-method	List-class
isEmpty,List-method	List-class
isRedundantHit	Hits-class
isSelfHit	Hits-class
isSequence	integer-utils
isSingleInteger	S4Vectors-internals
isSingleNumber	S4Vectors-internals
isSingleNumberOrNA	S4Vectors-internals
isSingleString	S4Vectors-internals
isSingleStringOrNA	S4Vectors-internals
isSorted	isSorted
isSorted,ANY-method	isSorted
isStrictlySorted	isSorted
isStrictlySorted,ANY-method	isSorted
isStrictlySorted,NSBS-method	subsetting-utils
isStrictlySorted,RangeNSBS-method	subsetting-utils
isStrictlySorted,Rle-method	Rle-class
isStrictlySorted,RleNSBS-method	Rle-class
isTRUEorFALSE	S4Vectors-internals
lapply,List-method	List-utils
lapply,SimpleList-method	SimpleList-class
length,LLint-method	LLint-class
length,NSBS-method	subsetting-utils
length,RangeNSBS-method	subsetting-utils
length,Rle-method	Rle-class
length,RleNSBS-method	Rle-class
length,TransposedDataFrame-method	TransposedDataFrame-class
length,Vector-method	Vector-class
lengths,Vector-method	Vector-class
levels	Factor-class
levels,Rle-method	Rle-utils
levels.Rle	Rle-utils
levels<-	Factor-class
levels<-,Factor-method	Factor-class
levels<-,Rle-method	Rle-utils
List	List-class
List-class	List-class
List-utils	List-utils
list_OR_List	List-class
list_OR_List-class	List-class
LLint	LLint-class
LLint-class	LLint-class
mad,Rle-method	Rle-utils
mad.Rle	Rle-utils
makeClassinfoRowForCompactPrinting	show-utils
makeNakedCharacterMatrixForDisplay	show-utils
makeNakedCharacterMatrixForDisplay,ANY-method	show-utils
makeNakedCharacterMatrixForDisplay,DataFrame-method	DataFrame-class
makeNakedCharacterMatrixForDisplay,Hits-method	Hits-class
makeNakedCharacterMatrixForDisplay,Pairs-method	Pairs-class
makeNakedCharacterMatrixForDisplay,TransposedDataFrame-method	TransposedDataFrame-class
makePrettyMatrixForCompactPrinting	show-utils
make_zero_col_DFrame	DataFrame-class
Map,List-method	List-utils
match	Vector-comparison
match,ANY,Rle-method	Rle-class
match,DataFrame,DataFrame-method	DataFrame-comparison
match,Factor,Factor-method	Factor-class
match,Hits,Hits-method	Hits-comparison
match,Pairs,Pairs-method	Pairs-class
match,Rle,ANY-method	Rle-class
match,Rle,Rle-method	Rle-class
match,Vector,Vector-method	Vector-comparison
matchIntegerPairs	integer-utils
matchIntegerQuads	integer-utils
Math,Rle-method	Rle-utils
Math2,Rle-method	Rle-utils
mcols	Vector-class
mcols,Vector-method	Vector-class
mcols<-	Vector-class
mcols<-,Vector-method	Vector-class
mean,Rle-method	Rle-utils
mean.Rle	Rle-utils
median,Rle-method	Rle-utils
median.Rle	Rle-utils
mendoapply	List-utils
merge	Vector-merge
merge,data.frame,DataFrame-method	DataFrame-combine
merge,DataFrame,data.frame-method	DataFrame-combine
merge,DataFrame,DataFrame-method	DataFrame-combine
merge,Vector,Vector-method	Vector-merge
mergeROWS	subsetting-utils
mergeROWS,ANY,ANY-method	subsetting-utils
mergeROWS,DataFrame,ANY-method	DataFrame-class
mergeROWS,Vector,ANY-method	Vector-class
metadata	Annotated-class
metadata,Annotated-method	Annotated-class
metadata<-	Annotated-class
metadata<-,Annotated-method	Annotated-class
mstack	stack-methods
mstack,DataFrame-method	stack-methods
mstack,Vector-method	stack-methods
mstack,vector-method	stack-methods
na.exclude,DataFrame-method	DataFrame-utils
na.omit,DataFrame-method	DataFrame-utils
names,Factor-method	Factor-class
names,Pairs-method	Pairs-class
names,SimpleList-method	SimpleList-class
names,TransposedDataFrame-method	TransposedDataFrame-class
names<-,Factor-method	Factor-class
names<-,Pairs-method	Pairs-class
names<-,SimpleList-method	SimpleList-class
names<-,TransposedDataFrame-method	TransposedDataFrame-class
NA_LLint_	LLint-class
nchar,Rle-method	Rle-utils
ncol,DataFrame-method	DataFrame-class
new2	S4Vectors-internals
nlevels	Factor-class
nlevels,Factor-method	Factor-class
nLnode	Hits-class
nLnode,Hits-method	Hits-class
nnode	Hits-class
nnode,SelfHits-method	Hits-class
normalizeDoubleBracketSubscript	subsetting-utils
normalizeSingleBracketReplacementValue	subsetting-utils
normalizeSingleBracketReplacementValue,ANY-method	subsetting-utils
normalizeSingleBracketSubscript	subsetting-utils
nRnode	Hits-class
nRnode,Hits-method	Hits-class
nrow,DataFrame-method	DataFrame-class
nrun	Rle-class
nrun,Rle-method	Rle-class
NSBS	subsetting-utils
NSBS,array-method	subsetting-utils
NSBS,character-method	subsetting-utils
NSBS,factor-method	subsetting-utils
NSBS,logical-method	subsetting-utils
NSBS,missing-method	subsetting-utils
NSBS,NSBS-method	subsetting-utils
NSBS,NULL-method	subsetting-utils
NSBS,numeric-method	subsetting-utils
NSBS,Rle-method	Rle-class
NSBS-class	subsetting-utils
Ops,LLint,LLint-method	LLint-class
Ops,LLint,numeric-method	LLint-class
Ops,numeric,LLint-method	LLint-class
Ops,Rle,Rle-method	Rle-utils
Ops,Rle,vector-method	Rle-utils
Ops,vector,Rle-method	Rle-utils
order,DataFrame-method	DataFrame-comparison
order,Hits-method	Hits-comparison
order,Pairs-method	Pairs-class
order,Rle-method	Rle-class
orderIntegerPairs	integer-utils
orderIntegerQuads	integer-utils
Pairs	Pairs-class
Pairs-class	Pairs-class
parallelVectorNames	Vector-class
parallelVectorNames,ANY-method	Vector-class
parallelVectorNames,List-method	List-class
parallel_slot_names	Vector-class
parallel_slot_names,Factor-method	Factor-class
parallel_slot_names,FilterRules-method	FilterRules-class
parallel_slot_names,Hits-method	Hits-class
parallel_slot_names,Pairs-method	Pairs-class
parallel_slot_names,SimpleList-method	SimpleList-class
parallel_slot_names,Vector-method	Vector-class
params	FilterRules-class
params,FilterClosure-method	FilterRules-class
paste,Rle-method	Rle-utils
pc	List-utils
pcompare	Vector-comparison
pcompare,ANY,ANY-method	Vector-comparison
pcompare,DataFrame,DataFrame-method	DataFrame-comparison
pcompare,Factor,Factor-method	Factor-class
pcompare,Hits,Hits-method	Hits-comparison
pcompare,numeric,numeric-method	Vector-comparison
pcompare,Pairs,Pairs-method	Pairs-class
pmax,Rle-method	Rle-utils
pmax.int,Rle-method	Rle-utils
pmin,Rle-method	Rle-utils
pmin.int,Rle-method	Rle-utils
Position,List-method	List-utils
printAtomicVectorInAGrid	S4Vectors-internals
quantile,Rle-method	Rle-utils
quantile.Rle	Rle-utils
queryHits	Hits-class
queryHits,HitsList-method	HitsList-class
queryLength	Hits-class
rank,Rle-method	Rle-class
rank,Vector-method	Vector-comparison
rbind,FilterMatrix-method	FilterMatrix-class
rbind,List-method	List-utils
rbind,RectangularData-method	RectangularData-class
rbind.RectangularData	RectangularData-class
RectangularData	RectangularData-class
RectangularData-class	RectangularData-class
recycleArg	S4Vectors-internals
recycleCharacterArg	S4Vectors-internals
recycleIntegerArg	S4Vectors-internals
recycleLogicalArg	S4Vectors-internals
recycleNumericArg	S4Vectors-internals
Reduce,List-method	List-utils
relistToClass	splitAsList
relistToClass,ANY-method	splitAsList
relistToClass,data.frame-method	DataFrame-utils
relistToClass,DataFrame-method	DataFrame-utils
relistToClass,Hits-method	HitsList-class
relistToClass,SortedByQueryHits-method	HitsList-class
remapHits	Hits-class
rename	Vector-class
rename,Vector-method	Vector-class
rename,vector-method	Vector-class
rep	Vector-class
rep,Rle-method	Rle-class
rep,Vector-method	Vector-class
rep.int	Vector-class
rep.int,Rle-method	Rle-class
rep.int,Vector-method	Vector-class
replaceCOLS	subsetting-utils
replaceROWS	subsetting-utils
replaceROWS,ANY,ANY-method	subsetting-utils
replaceROWS,DataFrame,ANY-method	DataFrame-class
replaceROWS,Rle,ANY-method	Rle-class
replaceROWS,Vector,ANY-method	Vector-class
rev	Vector-class
rev,Rle-method	Rle-class
rev,Vector-method	Vector-class
rev.Rle	Rle-class
rev.Vector	Vector-class
revElements	List-utils
revElements,List-method	List-utils
revElements,list-method	List-utils
Rle	Rle-class
Rle,ANY-method	Rle-class
Rle,Rle-method	Rle-class
Rle-class	Rle-class
Rle-runstat	Rle-runstat
Rle-utils	Rle-utils
ROWNAMES	RectangularData-class
ROWNAMES,ANY-method	RectangularData-class
rownames,DataFrame-method	DataFrame-class
ROWNAMES,RectangularData-method	RectangularData-class
ROWNAMES<-	RectangularData-class
ROWNAMES<-,ANY-method	RectangularData-class
rownames<-,DataFrame-method	DataFrame-class
ROWNAMES<-,RectangularData-method	RectangularData-class
runLength	Rle-class
runLength,Rle-method	Rle-class
runLength<-	Rle-class
runLength<-,Rle-method	Rle-class
runmean	Rle-runstat
runmean,Rle-method	Rle-runstat
runmed,Rle-method	Rle-runstat
runq	Rle-runstat
runq,Rle-method	Rle-runstat
runsum	Rle-runstat
runsum,Rle-method	Rle-runstat
runValue	Rle-class
runValue,Rle-method	Rle-class
runValue<-	Rle-class
runValue<-,Rle-method	Rle-class
runwtsum	Rle-runstat
runwtsum,Rle-method	Rle-runstat
safeExplode	character-utils
sameAsPreviousROW	Vector-comparison
sameAsPreviousROW,ANY-method	Vector-comparison
sameAsPreviousROW,DataFrame-method	DataFrame-comparison
sameAsPreviousROW,Pairs-method	Pairs-class
sapply,List-method	List-utils
sd,Rle-method	Rle-utils
second	Pairs-class
second,Pairs-method	Pairs-class
second<-	Pairs-class
second<-,Pairs-method	Pairs-class
selectHits	Hits-class
SelfHits	Hits-class
SelfHits-class	Hits-class
SelfHitsList	HitsList-class
SelfHitsList-class	HitsList-class
selfmatch	Vector-comparison
selfmatch,ANY-method	Vector-comparison
selfmatch,Factor-method	Factor-class
selfmatch,factor-method	Vector-comparison
selfmatch,Vector-method	Vector-comparison
selfmatchIntegerPairs	integer-utils
selfmatchIntegerQuads	integer-utils
setdiff,ANY,Rle-method	Rle-class
setdiff,Rle,ANY-method	Rle-class
setdiff,Rle,Rle-method	Rle-class
setdiff,Vector,Vector-method	Vector-setops
setdiff.Vector	Vector-setops
setequal,Vector,Vector-method	Vector-setops
setequal.Vector	Vector-setops
setListElement	subsetting-utils
setListElement,List-method	List-class
setListElement,list-method	subsetting-utils
setMethods	S4Vectors-internals
setValidity2	S4Vectors-internals
shiftApply	shiftApply-methods
shiftApply,Vector,Vector-method	shiftApply-methods
shiftApply,vector,vector-method	shiftApply-methods
shiftApply-methods	shiftApply-methods
show,DataFrame-method	DataFrame-class
show,Factor-method	Factor-class
show,FilterClosure-method	FilterRules-class
show,FilterMatrix-method	FilterMatrix-class
show,Hits-method	Hits-class
show,List-method	List-class
show,LLint-method	LLint-class
show,Pairs-method	Pairs-class
show,RangeNSBS-method	subsetting-utils
show,Rle-method	Rle-class
show,TransposedDataFrame-method	TransposedDataFrame-class
show-utils	show-utils
showAsCell	show-utils
showAsCell,ANY-method	show-utils
showAsCell,AsIs-method	show-utils
showAsCell,character-method	show-utils
showAsCell,data.frame-method	show-utils
showAsCell,DataFrame-method	DataFrame-class
showAsCell,Factor-method	Factor-class
showAsCell,List-method	List-class
showAsCell,list-method	show-utils
showAsCell,LLint-method	LLint-class
showAsCell,numeric-method	show-utils
SimpleList	SimpleList-class
SimpleList-class	SimpleList-class
smoothEnds,Rle-method	Rle-runstat
sort,DataFrame-method	DataFrame-comparison
sort,Rle-method	Rle-class
sort,SortedByQueryHits-method	Hits-class
sort,Vector-method	Vector-comparison
sort.DataFrame	DataFrame-comparison
sort.Rle	Rle-class
sort.Vector	Vector-comparison
SortedByQueryHits	Hits-class
SortedByQueryHits-class	Hits-class
SortedByQueryHitsList	HitsList-class
SortedByQueryHitsList-class	HitsList-class
SortedByQuerySelfHits	Hits-class
SortedByQuerySelfHits-class	Hits-class
SortedByQuerySelfHitsList	HitsList-class
SortedByQuerySelfHitsList-class	HitsList-class
space	HitsList-class
space,HitsList-method	HitsList-class
split	splitAsList
split,ANY,Vector-method	splitAsList
split,list,Vector-method	splitAsList
split,Vector,ANY-method	splitAsList
split,Vector,Vector-method	splitAsList
splitAsList	splitAsList
splitAsList,ANY,ANY-method	splitAsList
splitAsList,SortedByQueryHits,ANY-method	HitsList-class
stack,List-method	stack-methods
stack,matrix-method	stack-methods
stack-methods	stack-methods
start,Rle-method	Rle-class
sub,ANY,ANY,Rle-method	Rle-utils
subjectHits	Hits-class
subjectHits,HitsList-method	HitsList-class
subjectLength	Hits-class
subset	Vector-class
subset,RectangularData-method	RectangularData-class
subset,Vector-method	Vector-class
subset.Vector	Vector-class
subsetByFilter	FilterRules-class
subsetByFilter,ANY,FilterRules-method	FilterRules-class
subsetting-utils	subsetting-utils
substr,Rle-method	Rle-utils
substring,Rle-method	Rle-utils
summary,FilterMatrix-method	FilterMatrix-class
summary,FilterRules-method	FilterRules-class
summary,Hits-method	Hits-class
Summary,LLint-method	LLint-class
Summary,Rle-method	Rle-utils
summary,Rle-method	Rle-utils
summary,Vector-method	Vector-class
summary.Hits	Hits-class
summary.Rle	Rle-utils
summary.Vector	Vector-class
svn.time	character-utils
t,DataFrame-method	TransposedDataFrame-class
t,Hits-method	Hits-class
t,HitsList-method	HitsList-class
t,TransposedDataFrame-method	TransposedDataFrame-class
t.DataFrame	TransposedDataFrame-class
t.Hits	Hits-class
t.TransposedDataFrame	TransposedDataFrame-class
table,Rle-method	Rle-class
table,Vector-method	Vector-comparison
tabulate,Rle-method	Rle-class
tail	Vector-class
tail,RectangularData-method	RectangularData-class
tail,Vector-method	Vector-class
tail.RectangularData	RectangularData-class
tail.Vector	Vector-class
to	Hits-class
to,Hits-method	Hits-class
toListOfIntegerVectors	integer-utils
tolower,Rle-method	Rle-utils
toupper,Rle-method	Rle-utils
transform,DataFrame-method	DataFrame-utils
transform,Vector-method	Vector-class
transform.DataFrame	DataFrame-utils
transform.Vector	Vector-class
TransposedDataFrame	TransposedDataFrame-class
TransposedDataFrame-class	TransposedDataFrame-class
unfactor	Factor-class
unfactor,Factor-method	Factor-class
unfactor,factor-method	Factor-class
union,ANY,Rle-method	Rle-class
union,Rle,ANY-method	Rle-class
union,Rle,Rle-method	Rle-class
union,SortedByQueryHits,Hits-method	Hits-setops
union,Vector,Vector-method	Vector-setops
union.Vector	Vector-setops
unique,DataFrame-method	DataFrame-comparison
unique,Rle-method	Rle-class
unique,Vector-method	Vector-comparison
unique.DataFrame	DataFrame-comparison
unique.Vector	Vector-comparison
unlist,List-method	List-class
unname,Vector-method	Vector-class
unstrsplit	character-utils
unstrsplit,character-method	character-utils
unstrsplit,list-method	character-utils
updateObject,DataFrame-method	DataFrame-class
updateObject,Hits-method	Hits-class
updateObject,SimpleList-method	SimpleList-class
updateObject,Vector-method	Vector-class
values	Vector-class
values,Vector-method	Vector-class
values<-	Vector-class
values<-,Vector-method	Vector-class
var,Rle,missing-method	Rle-utils
var,Rle,Rle-method	Rle-utils
Vector	Vector-class
Vector-class	Vector-class
Vector-comparison	Vector-comparison
Vector-merge	Vector-merge
Vector-setops	Vector-setops
vector_OR_factor	S4Vectors-internals
vector_OR_factor-class	S4Vectors-internals
vector_OR_Vector	Vector-class
vector_OR_Vector-class	Vector-class
vertical_slot_names	RectangularData-class
vertical_slot_names,DataFrame-method	DataFrame-class
which,Rle-method	Rle-utils
which.max,Rle-method	Rle-utils
width,Rle-method	Rle-class
window	Vector-class
window,Vector-method	Vector-class
window.Vector	Vector-class
within,List-method	List-utils
wmsg	S4Vectors-internals
xtabs,DataFrame-method	DataFrame-utils
xtfrm,Factor-method	Factor-class
xtfrm,Rle-method	Rle-class
xtfrm,Vector-method	Vector-comparison
zipdown	zip-methods
zipdown,ANY-method	zip-methods
zipdown,List-method	zip-methods
zipup	zip-methods
zipup,ANY,ANY-method	zip-methods
zipup,Pairs,missing-method	Pairs-class
[	Vector-class
[,DataFrame-method	DataFrame-class
[,FilterMatrix-method	FilterMatrix-class
[,FilterRules-method	FilterRules-class
[,List-method	List-class
[,Rle-method	Rle-class
[,TransposedDataFrame-method	TransposedDataFrame-class
[,Vector-method	Vector-class
[<-,DataFrame-method	DataFrame-class
[<-,List-method	List-class
[<-,Rle,ANY-method	Rle-class
[<-,Vector-method	Vector-class
[[,DataFrame-method	DataFrame-class
[[,List-method	List-class
[[<-,DataFrame-method	DataFrame-class
[[<-,FilterRules-method	FilterRules-class
[[<-,List-method	List-class
