!,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
.Call2	S4Vectors-internals
<,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
==,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
>=,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,vector-method	aggregate-methods
aggregate-methods	aggregate-methods
aggregate.List	aggregate-methods
aggregate.Rle	aggregate-methods
aggregate.Vector	aggregate-methods
Annotated	Annotated-class
Annotated-class	Annotated-class
anyDuplicated,NSBS-method	subsetting-internals
anyDuplicated.NSBS	subsetting-internals
append,FilterRules,FilterRules-method	FilterRules-class
append,Vector,Vector-method	Vector-class
as.character,Vector-method	Vector-class
as.complex,Vector-method	Vector-class
as.data.frame,DataFrame-method	DataFrame-class
as.data.frame,List-method	List-class
as.data.frame,Rle-method	Rle-class
as.data.frame,Vector-method	Vector-class
as.data.frame.DataFrame	DataFrame-class
as.data.frame.List	List-class
as.data.frame.Rle	Rle-class
as.data.frame.Vector	Vector-class
as.double,Vector-method	Vector-class
as.env	DataTable-class
as.env,DataTable-method	DataTable-class
as.env,List-method	List-class
as.env,NULL-method	DataTable-class
as.env,Vector-method	Vector-class
as.factor,Rle-method	Rle-class
as.integer,NativeNSBS-method	subsetting-internals
as.integer,Vector-method	Vector-class
as.list,List-method	List-class
as.list,Rle-method	Rle-class
as.list,SimpleList-method	SimpleList-class
as.list.List	List-class
as.list.Rle	Rle-class
as.list.SimpleList	SimpleList-class
as.logical,Vector-method	Vector-class
as.matrix,DataFrame-method	DataFrame-class
as.matrix,Hits-method	Hits-class
as.numeric,Vector-method	Vector-class
as.raw,Vector-method	Vector-class
as.table,Hits-method	Hits-class
as.vector,Rle-method	Rle-class
as.vectorORfactor	Rle-class
as.vectorORfactor,Rle-method	Rle-class
by,DataTable-method	DataTable-class
c,FilterRules-method	FilterRules-class
c,Rle-method	Rle-class
c,SimpleList-method	SimpleList-class
cbind,DataFrame-method	DataFrame-class
cbind,DataTable-method	DataTable-class
cbind,FilterMatrix-method	FilterMatrix-class
characterORNULL	S4Vectors-internals
characterORNULL-class	S4Vectors-internals
chartr,ANY,ANY,Rle-method	Rle-utils
class:characterORNULL	S4Vectors-internals
class:DataFrame	DataFrame-class
class:DataTable	DataTable-class
class:DataTableORNULL	Vector-class
class:expressionORfunction	FilterRules-class
class:FilterRules	FilterRules-class
class:Hits	Hits-class
class:List	List-class
class:NSBS	subsetting-internals
class:Rle	Rle-class
class:SimpleList	SimpleList-class
class:Vector	Vector-class
class:vectorORfactor	S4Vectors-internals
classNameForDisplay	Vector-class
classNameForDisplay,ANY-method	Vector-class
classNameForDisplay,AsIs-method	Vector-class
classNameForDisplay,SimpleList-method	SimpleList-class
coerce,ANY,AsIs-method	DataFrame-class
coerce,ANY,DataFrame-method	DataFrame-class
coerce,ANY,List-method	List-class
coerce,ANY,SimpleList-method	SimpleList-class
coerce,ANY,vector-method	S4Vectors-internals
coerce,AsIs,DataFrame-method	DataFrame-class
coerce,character,Rle-method	Rle-class
coerce,complex,Rle-method	Rle-class
coerce,data.frame,DataFrame-method	DataFrame-class
coerce,DataFrame,data.frame-method	DataFrame-class
coerce,factor,Rle-method	Rle-class
coerce,function,FilterClosure-method	FilterRules-class
coerce,integer,DataFrame-method	DataFrame-class
coerce,integer,List-method	List-class
coerce,integer,Rle-method	Rle-class
coerce,List,data.frame-method	List-class
coerce,list,DataFrame-method	DataFrame-class
coerce,List,list-method	List-class
coerce,list,List-method	SimpleList-class
coerce,logical,Rle-method	Rle-class
coerce,matrix,DataFrame-method	DataFrame-class
coerce,NULL,DataFrame-method	DataFrame-class
coerce,numeric,Rle-method	Rle-class
coerce,raw,Rle-method	Rle-class
coerce,Rle,character-method	Rle-class
coerce,Rle,complex-method	Rle-class
coerce,Rle,data.frame-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,SimpleList,DataFrame-method	DataFrame-class
coerce,standardGeneric,FilterClosure-method	FilterRules-class
coerce,table,DataFrame-method	DataFrame-class
coerce,Vector,character-method	Vector-class
coerce,Vector,complex-method	Vector-class
coerce,Vector,data.frame-method	Vector-class
coerce,Vector,DataFrame-method	DataFrame-class
coerce,vector,DataFrame-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,Rle-method	Rle-class
coerce,Vector,vector-method	Vector-class
coerce,xtabs,DataFrame-method	DataFrame-class
colnames,DataFrame-method	DataFrame-class
colnames<-,DataFrame-method	DataFrame-class
compare	Vector-comparison
compare,Hits,Hits-method	Hits-comparison
complete.cases,DataTable-method	DataTable-class
Complex,Rle-method	Rle-utils
cor,Rle,Rle-method	Rle-utils
countMatches	Vector-comparison
countMatches,ANY,ANY-method	Vector-comparison
countQueryHits	Hits-class
countQueryHits,Hits-method	Hits-class
countSubjectHits	Hits-class
countSubjectHits,Hits-method	Hits-class
cov,Rle,Rle-method	Rle-utils
DataFrame	DataFrame-class
DataFrame-class	DataFrame-class
DataTable	DataTable-class
DataTable-class	DataTable-class
DataTableORNULL	Vector-class
DataTableORNULL-class	Vector-class
diff,Rle-method	Rle-utils
diff.Rle	Rle-utils
dim,DataTable-method	DataTable-class
dimnames,DataTable-method	DataTable-class
dimnames<-,DataTable-method	DataTable-class
duplicated,DataTable-method	DataTable-class
duplicated,Rle-method	Rle-class
duplicated,Vector-method	Vector-comparison
duplicated.DataTable	DataTable-class
duplicated.Rle	Rle-class
duplicated.Vector	Vector-comparison
elementLengths	List-class
elementLengths,ANY-method	List-class
elementLengths,List-method	List-class
elementMetadata	Vector-class
elementMetadata,Vector-method	Vector-class
elementMetadata<-	Vector-class
elementMetadata<-,Vector-method	Vector-class
elementType	List-class
elementType,List-method	List-class
elementType,vector-method	List-class
end,Rle-method	Rle-class
endoapply	List-utils
endoapply,data.frame-method	List-utils
endoapply,List-method	List-utils
endoapply,list-method	List-utils
endoapply,SimpleList-method	SimpleList-class
eval,FilterRules,ANY-method	FilterRules-class
evalSeparately	FilterRules-class
evalSeparately,FilterRules-method	FilterRules-class
expressionORfunction	FilterRules-class
expressionORfunction-class	FilterRules-class
extractROWS	subsetting-internals
extractROWS,ANY-method	subsetting-internals
extractROWS,Hits-method	Hits-class
extractROWS,NULL-method	subsetting-internals
extractROWS,Rle,ANY-method	Rle-class
extractROWS,Rle,WindowNSBS-method	Rle-class
Filter,List-method	List-utils
FilterMatrix	FilterMatrix-class
FilterMatrix-class	FilterMatrix-class
FilterRules	FilterRules-class
filterRules,FilterMatrix-method	FilterMatrix-class
FilterRules-class	FilterRules-class
Find,List-method	List-utils
findMatches	Vector-comparison
findMatches,ANY,ANY-method	Vector-comparison
findRun	Rle-class
findRun,Rle-method	Rle-class
fold	S4Vectors-internals
getListElement	subsetting-internals
get_showHeadLines	S4Vectors-internals
get_showTailLines	S4Vectors-internals
gsub,ANY,ANY,Rle-method	Rle-utils
Hits	Hits-class
Hits-class	Hits-class
Hits-comparison	Hits-comparison
Hits-setops	Hits-setops
ifelse,ANY,ANY,Rle-method	Rle-utils
ifelse,ANY,Rle,ANY-method	Rle-utils
ifelse,ANY,Rle,Rle-method	Rle-utils
intersect,ANY,Rle-method	Rle-class
intersect,Hits,Hits-method	Hits-setops
intersect,Rle,ANY-method	Rle-class
intersect,Rle,Rle-method	Rle-class
IQR,Rle-method	Rle-utils
is.na,DataTable-method	DataTable-class
is.na,Rle-method	Rle-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
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-internals
isTRUEorFALSE	S4Vectors-internals
lapply,List-method	List-utils
lapply,SimpleList-method	SimpleList-class
length,NSBS-method	subsetting-internals
length,Rle-method	Rle-class
length,SimpleList-method	SimpleList-class
length,Vector-method	Vector-class
lengths,Vector-method	Vector-class
levels,Rle-method	Rle-utils
levels.Rle	Rle-utils
levels<-,Rle-method	Rle-utils
List	List-class
List-class	List-class
List-utils	List-utils
mad,Rle-method	Rle-utils
mad.Rle	Rle-utils
Map,List-method	List-utils
match,Hits,Hits-method	Hits-comparison
match,Rle,ANY-method	Rle-class
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
mendoapply,data.frame-method	List-utils
mendoapply,List-method	List-utils
mendoapply,list-method	List-utils
mendoapply,SimpleList-method	SimpleList-class
merge,data.frame,DataTable-method	DataTable-class
merge,DataTable,data.frame-method	DataTable-class
merge,DataTable,DataTable-method	DataTable-class
metadata	Annotated-class
metadata,Annotated-method	Annotated-class
metadata<-	Annotated-class
metadata<-,Annotated-method	Annotated-class
na.exclude,DataTable-method	DataTable-class
na.omit,DataTable-method	DataTable-class
names,SimpleList-method	SimpleList-class
names<-,SimpleList-method	SimpleList-class
nchar,Rle-method	Rle-utils
ncol,DataFrame-method	DataFrame-class
NCOL,DataTable-method	DataTable-class
new2	S4Vectors-internals
normalizeDoubleBracketSubscript	subsetting-internals
normalizeSingleBracketReplacementValue	subsetting-internals
normalizeSingleBracketReplacementValue,ANY-method	subsetting-internals
normalizeSingleBracketSubscript	subsetting-internals
nrow,DataFrame-method	DataFrame-class
NROW,DataTable-method	DataTable-class
NROW,Vector-method	Vector-class
nrun	Rle-class
nrun,Rle-method	Rle-class
NSBS	subsetting-internals
NSBS,array-method	subsetting-internals
NSBS,character-method	subsetting-internals
NSBS,factor-method	subsetting-internals
NSBS,logical-method	subsetting-internals
NSBS,missing-method	subsetting-internals
NSBS,NSBS-method	subsetting-internals
NSBS,NULL-method	subsetting-internals
NSBS,numeric-method	subsetting-internals
NSBS-class	subsetting-internals
Ops,Rle,Rle-method	Rle-utils
Ops,Rle,vector-method	Rle-utils
Ops,vector,Rle-method	Rle-utils
order,Hits-method	Hits-comparison
order,Rle-method	Rle-class
parallelVectorNames	Vector-class
parallelVectorNames,ANY-method	Vector-class
params	FilterRules-class
params,FilterClosure-method	FilterRules-class
paste,Rle-method	Rle-utils
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,Hits-method	Hits-class
queryLength	Hits-class
queryLength,Hits-method	Hits-class
rank,Vector-method	Vector-comparison
rbind,DataFrame-method	DataFrame-class
rbind,DataTable-method	DataTable-class
rbind,FilterMatrix-method	FilterMatrix-class
recycleIntegerArg	S4Vectors-internals
recycleNumericArg	S4Vectors-internals
Reduce,List-method	List-utils
remapHits	Hits-class
rename	Vector-class
rename,Vector-method	Vector-class
rename,vector-method	Vector-class
rep,Rle-method	Rle-class
rep.int,Rle-method	Rle-class
replaceROWS	subsetting-internals
replaceROWS,ANY-method	subsetting-internals
replaceROWS,NULL-method	subsetting-internals
replaceROWS,Vector-method	Vector-class
rev,Rle-method	Rle-class
rev.Rle	Rle-class
revElements	List-utils
revElements,List-method	List-utils
revElements,list-method	List-utils
Rle	Rle-class
Rle,missing,missing-method	Rle-class
Rle,vectorORfactor,integer-method	Rle-class
Rle,vectorORfactor,missing-method	Rle-class
Rle,vectorORfactor,numeric-method	Rle-class
Rle-class	Rle-class
Rle-runstat	Rle-runstat
Rle-utils	Rle-utils
ROWNAMES	DataTable-class
ROWNAMES,ANY-method	DataTable-class
rownames,DataFrame-method	DataFrame-class
ROWNAMES,DataTable-method	DataTable-class
ROWNAMES,Vector-method	Vector-class
rownames<-,DataFrame-method	DataFrame-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	str-utils
sapply,List-method	List-utils
sd,Rle-method	Rle-utils
selfmatch	Vector-comparison
selfmatch,ANY-method	Vector-comparison
setdiff,ANY,Rle-method	Rle-class
setdiff,Hits,Hits-method	Hits-setops
setdiff,Rle,ANY-method	Rle-class
setdiff,Rle,Rle-method	Rle-class
setListElement	subsetting-internals
setMethods	S4Vectors-internals
setops-methods	Hits-setops
setValidity2	S4Vectors-internals
shiftApply,Rle,Rle-method	Rle-class
show,DataTable-method	DataTable-class
show,FilterClosure-method	FilterRules-class
show,FilterMatrix-method	FilterMatrix-class
show,Hits-method	Hits-class
show,List-method	List-class
show,Rle-method	Rle-class
showAsCell	Vector-class
showAsCell,ANY-method	Vector-class
showAsCell,Rle-method	Rle-class
showAsCell,Vector-method	Vector-class
SimpleList	SimpleList-class
SimpleList-class	SimpleList-class
smoothEnds,Rle-method	Rle-runstat
sort,Rle-method	Rle-class
sort,Vector-method	Vector-comparison
sort.Rle	Rle-class
sort.Vector	Vector-comparison
split	split-methods
split,ANY,Vector-method	split-methods
split,list,Vector-method	split-methods
split,Vector,ANY-method	split-methods
split,Vector,Vector-method	split-methods
split-methods	split-methods
start,Rle-method	Rle-class
strsplitAsListOfIntegerVectors	str-utils
sub,ANY,ANY,Rle-method	Rle-utils
subjectHits	Hits-class
subjectHits,Hits-method	Hits-class
subjectLength	Hits-class
subjectLength,Hits-method	Hits-class
subset,DataTable-method	DataTable-class
subsetByFilter	FilterRules-class
subsetByFilter,ANY,FilterRules-method	FilterRules-class
subsetting-internals	subsetting-internals
substr,Rle-method	Rle-utils
substring,Rle-method	Rle-utils
summary,FilterMatrix-method	FilterMatrix-class
summary,FilterRules-method	FilterRules-class
Summary,Rle-method	Rle-utils
summary,Rle-method	Rle-utils
summary.Rle	Rle-utils
svn.time	str-utils
t,Hits-method	Hits-class
table,Rle-method	Rle-class
table,Vector-method	Vector-comparison
tolower,Rle-method	Rle-utils
toupper,Rle-method	Rle-utils
union,ANY,Rle-method	Rle-class
union,Hits,Hits-method	Hits-setops
union,Rle,ANY-method	Rle-class
union,Rle,Rle-method	Rle-class
unique,DataTable-method	DataTable-class
unique,Rle-method	Rle-class
unique,Vector-method	Vector-comparison
unique.DataTable	DataTable-class
unique.Rle	Rle-class
unique.Vector	Vector-comparison
unlist,List-method	List-class
unstrsplit	str-utils
unstrsplit,character-method	str-utils
unstrsplit,list-method	str-utils
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
vectorORfactor	S4Vectors-internals
vectorORfactor-class	S4Vectors-internals
which,Rle-method	Rle-utils
which.max,Rle-method	Rle-utils
width,Rle-method	Rle-class
within,List-method	List-utils
wmsg	S4Vectors-internals
xtabs,DataTable-method	DataTable-class
[,DataFrame-method	DataFrame-class
[,FilterMatrix-method	FilterMatrix-class
[,FilterRules-method	FilterRules-class
[,List-method	List-class
[,Rle-method	Rle-class
[,Vector-method	Vector-class
[<-,DataFrame-method	DataFrame-class
[<-,List-method	List-class
[<-,Rle-method	Rle-class
[<-,Vector-method	Vector-class
[[,List-method	List-class
[[<-,DataFrame-method	DataFrame-class
[[<-,FilterRules-method	FilterRules-class
[[<-,List-method	List-class
