plyinteractions-package	plyinteractions-package
$,GInteractions-method	ginteractions-getters
add_pairdist	add-pairdist
anchor.AnchoredPinnedGInteractions	ginteractions-anchor
anchors,DelegatingGInteractions-method	delegating-ginteractions-methods
anchors1	ginteractions-getters
anchors1,DelegatingGInteractions-method	delegating-ginteractions-methods
anchors1,GInteractions-method	ginteractions-getters
anchors2	ginteractions-getters
anchors2,DelegatingGInteractions-method	delegating-ginteractions-methods
anchors2,GInteractions-method	ginteractions-getters
anchor_3p.AnchoredPinnedGInteractions	ginteractions-anchor
anchor_3p.PinnedGInteractions	ginteractions-anchor
anchor_5p.AnchoredPinnedGInteractions	ginteractions-anchor
anchor_5p.PinnedGInteractions	ginteractions-anchor
anchor_center.AnchoredPinnedGInteractions	ginteractions-anchor
anchor_center.PinnedGInteractions	ginteractions-anchor
anchor_end.AnchoredPinnedGInteractions	ginteractions-anchor
anchor_end.PinnedGInteractions	ginteractions-anchor
anchor_start.AnchoredPinnedGInteractions	ginteractions-anchor
anchor_start.PinnedGInteractions	ginteractions-anchor
annotate	ginteractions-annotate
annotate,GInteractions,GRanges,character-method	ginteractions-annotate
annotate_directed	ginteractions-annotate
annotate_directed,GInteractions,GRanges,character-method	ginteractions-annotate
arrange.GInteractions	dplyr-arrange
as_ginteractions	ginteractions-construct
ce10_ARCC	plyinteractions-data
ce10_REs	plyinteractions-data
count.GInteractions	dplyr-count
count.GroupedGInteractions	dplyr-count
count_overlaps.GInteractions	ginteractions-count-overlaps
count_overlaps.PinnedGInteractions	ginteractions-count-overlaps
count_overlaps_directed.GInteractions	ginteractions-count-overlaps
count_overlaps_directed.PinnedGInteractions	ginteractions-count-overlaps
delegating-ginteractions-methods	delegating-ginteractions-methods
dplyr-arrange	dplyr-arrange
dplyr-count	dplyr-count
dplyr-filter	dplyr-filter
dplyr-group_by	dplyr-group_by
dplyr-mutate	dplyr-mutate
dplyr-rename	dplyr-rename
dplyr-select	dplyr-select
dplyr-slice	dplyr-slice
dplyr-summarise	dplyr-summarize
dplyr-summarize	dplyr-summarize
end1	ginteractions-getters
end1,DelegatingGInteractions-method	delegating-ginteractions-methods
end1,GInteractions-method	ginteractions-getters
end2	ginteractions-getters
end2,DelegatingGInteractions-method	delegating-ginteractions-methods
end2,GInteractions-method	ginteractions-getters
filter.GInteractions	dplyr-filter
filter_by_non_overlaps.GInteractions	ginteractions-filter-overlaps
filter_by_non_overlaps.PinnedGInteractions	ginteractions-filter-overlaps
filter_by_overlaps.GInteractions	ginteractions-filter-overlaps
filter_by_overlaps.PinnedGInteractions	ginteractions-filter-overlaps
find_overlaps.GInteractions	ginteractions-find-overlaps
find_overlaps.PinnedGInteractions	ginteractions-find-overlaps
find_overlaps_directed.GInteractions	ginteractions-find-overlaps
find_overlaps_directed.PinnedGInteractions	ginteractions-find-overlaps
first<-,GInteractions-method	ginteractions-setters
flank_downstream	plyinteractions-flank
flank_downstream.PinnedGInteractions	plyinteractions-flank
flank_downstream.Ranges	plyinteractions-flank
flank_left	plyinteractions-flank
flank_left.PinnedGInteractions	plyinteractions-flank
flank_left.Ranges	plyinteractions-flank
flank_right	plyinteractions-flank
flank_right.PinnedGInteractions	plyinteractions-flank
flank_right.Ranges	plyinteractions-flank
flank_upstream	plyinteractions-flank
flank_upstream.PinnedGInteractions	plyinteractions-flank
flank_upstream.Ranges	plyinteractions-flank
ginteractions-anchor	ginteractions-anchor
ginteractions-annotate	ginteractions-annotate
ginteractions-count-overlaps	ginteractions-count-overlaps
ginteractions-export	ginteractions-export
ginteractions-filter-overlaps	ginteractions-filter-overlaps
ginteractions-find-overlaps	ginteractions-find-overlaps
ginteractions-getters	ginteractions-getters
ginteractions-join-overlap-left	ginteractions-join-overlap-left
ginteractions-pin	ginteractions-pin
ginteractions-setters	ginteractions-setters
GM12878_HiCCUPS	plyinteractions-data
group-group_data	group-group_data
groups.GroupedGInteractions	group-group_data
group_by.DelegatingGInteractions	dplyr-group_by
group_by.GInteractions	dplyr-group_by
group_data.GroupedGInteractions	group-group_data
group_indices.GroupedGInteractions	group-group_data
group_keys.GroupedGInteractions	group-group_data
group_size.GroupedGInteractions	group-group_data
group_vars.GInteractions	group-group_data
group_vars.GroupedGInteractions	group-group_data
join_overlap_left.GInteractions	ginteractions-join-overlap-left
join_overlap_left.PinnedGInteractions	ginteractions-join-overlap-left
join_overlap_left_directed.GInteractions	ginteractions-join-overlap-left
join_overlap_left_directed.PinnedGInteractions	ginteractions-join-overlap-left
mcols,DelegatingGInteractions-method	delegating-ginteractions-methods
mutate.GInteractions	dplyr-mutate
n_groups.GroupedGInteractions	group-group_data
pair_granges	pair-granges
pin	ginteractions-pin
pin,AnchoredPinnedGInteractions,character-method	ginteractions-pin
pin,AnchoredPinnedGInteractions,numeric-method	ginteractions-pin
pin,GInteractions,character-method	ginteractions-pin
pin,GInteractions,numeric-method	ginteractions-pin
pin,GroupedGInteractions,character-method	ginteractions-pin
pin,GroupedGInteractions,numeric-method	ginteractions-pin
pin,PinnedGInteractions,character-method	ginteractions-pin
pin,PinnedGInteractions,missing-method	ginteractions-pin
pin,PinnedGInteractions,numeric-method	ginteractions-pin
pinned_anchors	ginteractions-pin
pinned_anchors,AnchoredPinnedGInteractions-method	ginteractions-pin
pinned_anchors,PinnedGInteractions-method	ginteractions-pin
pin_anchors1	ginteractions-pin
pin_anchors2	ginteractions-pin
pin_by	ginteractions-pin
pin_first	ginteractions-pin
pin_second	ginteractions-pin
plyinteractions	plyinteractions-package
plyinteractions-data	plyinteractions-data
plyinteractions-flank	plyinteractions-flank
plyinteractions-shift	plyinteractions-shift
plyranges-stretch	plyranges-stretch
ranges1	ginteractions-getters
ranges1,DelegatingGInteractions-method	delegating-ginteractions-methods
ranges1,GInteractions-method	ginteractions-getters
ranges2	ginteractions-getters
ranges2,DelegatingGInteractions-method	delegating-ginteractions-methods
ranges2,GInteractions-method	ginteractions-getters
regions,DelegatingGInteractions-method	delegating-ginteractions-methods
rename.GInteractions	dplyr-rename
replace_anchors	replace_anchors
replace_anchors,AnchoredPinnedGInteractions,missing,GRanges-method	replace_anchors
replace_anchors,AnchoredPinnedGInteractions,numeric,GRanges-method	replace_anchors
replace_anchors,GInteractions,character,GenomicRanges-method	replace_anchors
replace_anchors,GInteractions,numeric,GenomicRanges-method	replace_anchors
replace_anchors,PinnedGInteractions,missing,GenomicRanges-method	replace_anchors
second<-,GInteractions-method	ginteractions-setters
select.GInteractions	dplyr-select
seqinfo,DelegatingGInteractions-method	delegating-ginteractions-methods
seqnames1	ginteractions-getters
seqnames1,DelegatingGInteractions-method	delegating-ginteractions-methods
seqnames1,GInteractions-method	ginteractions-getters
seqnames2	ginteractions-getters
seqnames2,DelegatingGInteractions-method	delegating-ginteractions-methods
seqnames2,GInteractions-method	ginteractions-getters
set_end1	ginteractions-setters
set_end1,GInteractions,numeric-method	ginteractions-setters
set_end2	ginteractions-setters
set_end2,GInteractions,numeric-method	ginteractions-setters
set_seqnames1	ginteractions-setters
set_seqnames1,GInteractions,factor-method	ginteractions-setters
set_seqnames2	ginteractions-setters
set_seqnames2,GInteractions,factor-method	ginteractions-setters
set_start1	ginteractions-setters
set_start1,GInteractions,numeric-method	ginteractions-setters
set_start2	ginteractions-setters
set_start2,GInteractions,numeric-method	ginteractions-setters
set_strand1	ginteractions-setters
set_strand1,GInteractions,character-method	ginteractions-setters
set_strand2	ginteractions-setters
set_strand2,GInteractions,character-method	ginteractions-setters
set_width1	ginteractions-setters
set_width1,AnchoredPinnedGInteractions,numeric-method	ginteractions-setters
set_width1,GInteractions,numeric-method	ginteractions-setters
set_width2	ginteractions-setters
set_width2,AnchoredPinnedGInteractions,numeric-method	ginteractions-setters
set_width2,GInteractions,numeric-method	ginteractions-setters
shift_downstream	plyinteractions-shift
shift_downstream.PinnedGInteractions	plyinteractions-shift
shift_downstream.Ranges	plyinteractions-shift
shift_left	plyinteractions-shift
shift_left.PinnedGInteractions	plyinteractions-shift
shift_left.Ranges	plyinteractions-shift
shift_right	plyinteractions-shift
shift_right.PinnedGInteractions	plyinteractions-shift
shift_right.Ranges	plyinteractions-shift
shift_upstream	plyinteractions-shift
shift_upstream.PinnedGInteractions	plyinteractions-shift
shift_upstream.Ranges	plyinteractions-shift
show,AnchoredPinnedGInteractions-method	show-GInteractions
show,DelegatingGInteractions-method	delegating-ginteractions-methods
show,GInteractions-method	show-GInteractions
show,GroupedGInteractions-method	show-GInteractions
show,PinnedGInteractions-method	show-GInteractions
show-GInteractions	show-GInteractions
slice.GInteractions	dplyr-slice
start1	ginteractions-getters
start1,DelegatingGInteractions-method	delegating-ginteractions-methods
start1,GInteractions-method	ginteractions-getters
start2	ginteractions-getters
start2,DelegatingGInteractions-method	delegating-ginteractions-methods
start2,GInteractions-method	ginteractions-getters
strand1	ginteractions-getters
strand1,DelegatingGInteractions-method	delegating-ginteractions-methods
strand1,GInteractions-method	ginteractions-getters
strand2	ginteractions-getters
strand2,DelegatingGInteractions-method	delegating-ginteractions-methods
strand2,GInteractions-method	ginteractions-getters
stretch.AnchoredPinnedGInteractions	plyranges-stretch
stretch.PinnedGInteractions	plyranges-stretch
summarise.GroupedGInteractions	dplyr-summarize
summarize.GroupedGInteractions	dplyr-summarize
tally.GroupedGInteractions	dplyr-count
unanchor.AnchoredPinnedGInteractions	ginteractions-anchor
ungroup.GroupedGInteractions	dplyr-group_by
unpin	ginteractions-pin
unpin,AnchoredPinnedGInteractions-method	ginteractions-pin
unpin,GInteractions-method	ginteractions-pin
unpin,PinnedGInteractions-method	ginteractions-pin
width1	ginteractions-getters
width1,DelegatingGInteractions-method	delegating-ginteractions-methods
width1,GInteractions-method	ginteractions-getters
width2	ginteractions-getters
width2,DelegatingGInteractions-method	delegating-ginteractions-methods
width2,GInteractions-method	ginteractions-getters
write_bedpe	ginteractions-export
write_pairs	ginteractions-export
