afmhotrColors	palettes
anchors	Contacts
anchors,Contacts-method	Contacts
are_contacts	checks
asGInteractions	utils
autocorrelate	arithmetics
bbrColors	palettes
bins	Contacts
bins,Contacts-method	Contacts
bwrColors	palettes
centros_yeast	datasets
char2coords	utils
check_cool_file	checks
check_cool_format	checks
check_resolution	checks
cisTransRatio	cisTransRatio
cm2matrix	parse
Contacts	Contacts
Contacts-class	Contacts
contacts_yeast	datasets
contacts_yeast_eco1	datasets
cool2gi	parse
cool2seqinfo	parse
coords2char	utils
detrend	arithmetics
distanceLaw	Ps
divide	arithmetics
fetchCool	parse
fileName	Contacts
fileName,Contacts-method	Contacts
focus	Contacts
focus,Contacts-method	Contacts
focus<-	Contacts
focus<-,Contacts,character-method	Contacts
fullContactInteractions	utils
full_contacts_yeast	datasets
getAnchors	parse
getCounts	parse
getCountsFromPair	parse
getHicStats	utils
ggMatrix	Contacts-plot
ggthemeHiContacts	ggplot2-extra
gi2cm	parse
HiContacts package	HiContacts-package
interactions	Contacts
interactions,Contacts-method	Contacts
interactions<-	Contacts
interactions<-,Contacts,GInteractions-method	Contacts
is_comparable	checks
is_cool	checks
is_mcool	checks
is_same_bins	checks
is_same_regions	checks
is_same_resolution	checks
is_same_seqinfo	checks
is_square	checks
is_symmetrical	checks
length	Contacts
length,Contacts-method	Contacts
localDistanceLaw	Ps
lsCoolFiles	parse
lsCoolResolutions	parse
merge	arithmetics
metadata<-	Contacts
metadata<-,Contacts,list-method	Contacts
pairs2gi	parse
pairsFile	Contacts
pairsFile,Contacts-method	Contacts
pairsFile<-	Contacts
pairsFile<-,Contacts,character-method	Contacts
peekCool	parse
plot4C	virtual4C-plot
plotMatrix	Contacts-plot
plotPs	Ps-plot
plotPsSlope	Ps-plot
PsBreaks	Ps
regions	Contacts
regions,Contacts-method	Contacts
resolution	Contacts
resolution,Contacts-method	Contacts
resolutions	Contacts
resolutions,Contacts-method	Contacts
scores	Contacts
scores,Contacts,character-method	Contacts
scores,Contacts,missing-method	Contacts
scores,Contacts,numeric-method	Contacts
scores<-	Contacts
scores<-,Contacts,character,numeric-method	Contacts
sdiag<-	utils
seqinfo,Contacts-method	Contacts
serpentinify	arithmetics
setAs	Contacts
setAs,Contacts-method	Contacts
show	Contacts
show,Contacts-method	Contacts
sortPairs	utils
splitCoords	utils
summary	Contacts
summary,Contacts-method	Contacts
topologicalFeatures	Contacts
topologicalFeatures,Contacts,character-method	Contacts
topologicalFeatures,Contacts,missing-method	Contacts
topologicalFeatures,Contacts,numeric-method	Contacts
topologicalFeatures<-	Contacts
topologicalFeatures<-,Contacts,character,GRangesOrGInteractions-method	Contacts
virtual4C	virtual4C
[	Contacts
[,Contacts,character,ANY,ANY-method	Contacts
[,Contacts,logical,ANY,ANY-method	Contacts
[,Contacts,numeric,ANY,ANY-method	Contacts
