genomeIntervals-package	genomeIntervals-package
$,Genome_intervals-method	Genome_intervals-class
$<-,Genome_intervals-method	Genome_intervals-class
.readGff3	genomeIntervals-readGff3
annotation	Genome_intervals-class
annotation,Genome_intervals-method	Genome_intervals-class
annotation<-	Genome_intervals-class
annotation<-,Genome_intervals-method	Genome_intervals-class
as	Genome_intervals-coercion-methods
as,Genome_intervals,GRangesList-method	Genome_intervals-coercion-methods
as,Genome_intervals-method	Genome_intervals-coercion-methods
c	c.Genome_intervals
c,Genome_intervals-method	c.Genome_intervals
c,Genome_intervals_stranded-method	c.Genome_intervals
coerce,Genome_intervals,character-method	Genome_intervals-class
coerce,Genome_intervals,data.frame-method	Genome_intervals-class
coerce,Genome_intervals,GRanges-method	Genome_intervals-coercion-methods
coerce,Genome_intervals,GRangesList-method	Genome_intervals-coercion-methods
coerce,Genome_intervals,Intervals_full-method	Genome_intervals-class
coerce,Genome_intervals_stranded,character-method	Genome_intervals_stranded-class
core_annotated	core_annotated
core_annotated,Genome_intervals-method	core_annotated
core_annotated,Genome_intervals_stranded-method	core_annotated
distance_to_nearest	distance_to_nearest-methods
distance_to_nearest,Genome_intervals,Genome_intervals-method	distance_to_nearest-methods
distance_to_nearest,Genome_intervals_stranded,Genome_intervals_stranded-method	distance_to_nearest-methods
GenomeIntervals	GenomeIntervals-constructor
genomeIntervals	genomeIntervals-package
genomeIntervals coercion methods	Genome_intervals-coercion-methods
GenomeIntervals-constructor	GenomeIntervals-constructor
Genome_intervals deprecated functions	Genome_intervals-deprecated
Genome_intervals-class	Genome_intervals-class
Genome_intervals-ordering	Genome_intervals-ordering
Genome_intervals_stranded-class	Genome_intervals_stranded-class
gen_ints	gen_ints
getGffAttribute	getGffAttribute
i	gen_ints
interval_complement	interval_set_operations-methods
interval_complement,Genome_intervals-method	interval_set_operations-methods
interval_complement,Genome_intervals_stranded-method	interval_set_operations-methods
interval_intersection	interval_set_operations-methods
interval_intersection,Genome_intervals-method	interval_set_operations-methods
interval_intersection,Genome_intervals_stranded-method	interval_set_operations-methods
interval_overlap	interval_overlap-methods
interval_overlap,ANY,missing-method	interval_overlap-methods
interval_overlap,Genome_intervals,Genome_intervals-method	interval_overlap-methods
interval_overlap,Genome_intervals_stranded,Genome_intervals_stranded-method	interval_overlap-methods
interval_overlap,missing,ANY-method	interval_overlap-methods
interval_union	interval_set_operations-methods
interval_union,Genome_intervals-method	interval_set_operations-methods
interval_union,Genome_intervals_stranded-method	interval_set_operations-methods
inter_base	Genome_intervals-class
inter_base,Genome_intervals-method	Genome_intervals-class
inter_base<-	Genome_intervals-class
inter_base<-,Genome_intervals-method	Genome_intervals-class
j	gen_ints
k	gen_ints
order	Genome_intervals-ordering
order,Genome_intervals-method	Genome_intervals-ordering
order,Genome_intervals_stranded-method	Genome_intervals-ordering
parseGffAttributes	parseGffAttributes
rank	Genome_intervals-ordering
rank,Genome_intervals-method	Genome_intervals-ordering
rank,Genome_intervals_stranded-method	Genome_intervals-ordering
readBasePairFeaturesGff3	genomeIntervals-readGff3
readBasePairFeaturesGff3,character-method	genomeIntervals-readGff3
readGff3	genomeIntervals-readGff3
readGff3,character-method	genomeIntervals-readGff3
readZeroLengthFeaturesGff3	genomeIntervals-readGff3
readZeroLengthFeaturesGff3,character-method	genomeIntervals-readGff3
seqnames,Genome_intervals-method	Genome_intervals-class
seqnames<-,Genome_intervals-method	Genome_intervals-class
seq_name	Genome_intervals-deprecated
seq_name,Genome_intervals-method	Genome_intervals-deprecated
seq_name<-	Genome_intervals-deprecated
seq_name<-,Genome_intervals-method	Genome_intervals-deprecated
show,Genome_intervals-method	Genome_intervals-class
size,Genome_intervals-method	Genome_intervals-class
sort	Genome_intervals-ordering
sort,Genome_intervals-method	Genome_intervals-ordering
sort,Genome_intervals_stranded-method	Genome_intervals-ordering
strand	Genome_intervals_stranded-class
strand,Genome_intervals_stranded-method	Genome_intervals_stranded-class
strand<-	Genome_intervals_stranded-class
strand<-,Genome_intervals_stranded,ANY-method	Genome_intervals-class
strand<-,Genome_intervals_stranded-method	Genome_intervals_stranded-class
type<-,Genome_intervals-method	Genome_intervals-class
which_nearest,Genome_intervals,Genome_intervals-method	Genome_intervals-class
width,Genome_intervals-method	Genome_intervals-class
writeGff3	genomeIntervals-readGff3
writeGff3,data.frame-method	genomeIntervals-readGff3
writeGff3,Genome_intervals-method	genomeIntervals-readGff3
xtfrm	Genome_intervals-ordering
xtfrm,Genome_intervals-method	Genome_intervals-ordering
xtfrm,Genome_intervals_stranded-method	Genome_intervals-ordering
[,Genome_intervals,ANY-method	Genome_intervals-class
[,Genome_intervals-method	Genome_intervals-class
[<-,Genome_intervals,ANY,missing,Genome_intervals-method	Genome_intervals-class
[[,Genome_intervals,ANY,ANY-method	Genome_intervals-class
[[,Genome_intervals,ANY-method	Genome_intervals-class
[[,Genome_intervals-method	Genome_intervals-class
[[<-,Genome_intervals,ANY,ANY-method	Genome_intervals-class
[[<-,Genome_intervals,ANY-method	Genome_intervals-class
[[<-,Genome_intervals-method	Genome_intervals-class
