$,HiCExperiment-method	HiCExperiment
$<-,HiCExperiment-method	HiCExperiment
.check_cool_file	checks
.check_cool_format	checks
.check_hicpro_files	checks
.check_hic_file	checks
.check_hic_format	checks
.check_resolution	checks
.check_scores	checks
.cool2gi	parse-cool
.cool2seqinfo	parse-cool
.df2symmmat	utils
.dumpCool	parse-cool
.dumpHic	parse-hic
.dumpHicpro	parse-hicpro
.fetchCool	parse-cool
.fixRegions	utils
.getCoolAnchors	parse-cool
.getCounts	parse-cool
.getCountsFromPair	parse-cool
.getHicAnchors	parse-hic
.getHicproAnchors	parse-hicpro
.hic2gi	parse-hic
.hic2seqinfo	parse-hic
.hicpro2gi	parse-hicpro
.hicpro2seqinfo	parse-hicpro
.is_cool	checks
.is_hic	checks
.is_hicpro_matrix	checks
.is_hicpro_regions	checks
.is_mcool	checks
.is_square	checks
.lsCoolFiles	parse-cool
.lsCoolResolutions	parse-cool
.lsHicResolutions	parse-hic
.multi2DQuery	multi2Query
.pairs2gi	parse-pairs
AggrHiCExperiment	AggrHiCExperiment
AggrHiCExperiment-class	AggrHiCExperiment
AllGenerics	AllGenerics
anchors,HiCExperiment-method	HiCExperiment
as	as
as.data.frame,HiCExperiment-method	as
as.matrix,HiCExperiment-method	as
asGInteractions	utils
availableChromosomes	AllGenerics
availableChromosomes,ANY-method	import-methods
availableChromosomes,CoolFile-method	import-methods
availableChromosomes,HicFile-method	import-methods
availableChromosomes,HicproFile-method	import-methods
availableResolutions	AllGenerics
availableResolutions,ANY-method	import-methods
availableResolutions,CoolFile-method	import-methods
availableResolutions,HicFile-method	import-methods
availableResolutions,HicproFile-method	import-methods
bins	AllGenerics
bins,HiCExperiment-method	HiCExperiment
centros_yeast	data
char2coords	utils
checks	checks
cis	AllGenerics
cis,HiCExperiment-method	HiCExperiment
cm2matrix	as
coerce,HiCExperiment,ContactMatrix-method	as
coerce,HiCExperiment,data.frame-method	as
coerce,HiCExperiment,GInteractions-method	as
coerce,HiCExperiment,InteractionSet-method	as
coerce,HiCExperiment,matrix-method	as
ContactsFile	ContactsFile-class
ContactsFile-class	ContactsFile-class
ContactsFile-methods	ContactsFile-class
contacts_yeast	data
contacts_yeast_eco1	data
CoolFile	CoolFile-class
CoolFile-class	CoolFile-class
CoolFile-methods	CoolFile-class
coords2char	utils
data	data
detrendingModel	utils
df2gi	as
distanceDecay	utils
fileName,HiCExperiment-method	HiCExperiment
focus	AllGenerics
focus,HiCExperiment-method	HiCExperiment
focus<-	AllGenerics
focus<-,HiCExperiment,character-method	HiCExperiment
focus<-,HiCExperiment-method	HiCExperiment
gi2cm	as
HiCExperiment	HiCExperiment
HiCExperiment utils	utils
HiCExperiment-class	HiCExperiment
HicFile	HicFile-class
HicFile-class	HicFile-class
HicFile-methods	HicFile-class
HicproFile	HicproFile-class
HicproFile-class	HicproFile-class
HicproFile-methods	HicproFile-class
import	import-methods
import,CoolFile,ANY,ANY-method	import-methods
import,CoolFile-method	import-methods
import,HicFile,ANY,ANY-method	import-methods
import,HicFile-method	import-methods
import,HicproFile,ANY,ANY-method	import-methods
import,HicproFile-method	import-methods
import,PairsFile,ANY,ANY-method	import-methods
import,PairsFile-method	import-methods
import-methods	import-methods
interactions,HiCExperiment-method	HiCExperiment
interactions<-,HiCExperiment,GInteractions-method	HiCExperiment
interactions<-,HiCExperiment-method	HiCExperiment
length,HiCExperiment-method	HiCExperiment
makeHiCExperimentFromGInteractions	HiCExperiment
McoolFile-class	CoolFile-class
metadata	reexports
metadata<-	AllGenerics
metadata<-,ContactsFile,list-method	ContactsFile-class
metadata<-,ContactsFile-method	ContactsFile-class
metadata<-,HiCExperiment,list-method	HiCExperiment
metadata<-,HiCExperiment-method	HiCExperiment
multi2Query	multi2Query
PairsFile	PairsFile-class
pairsFile	AllGenerics
pairsFile,ContactsFile-method	ContactsFile-class
pairsFile,HiCExperiment-method	HiCExperiment
pairsFile,PairsFile-method	PairsFile-class
PairsFile-class	PairsFile-class
pairsFile<-	AllGenerics
pairsFile<-,HiCExperiment,character-method	HiCExperiment
pairsFile<-,HiCExperiment-method	HiCExperiment
parse-cool	parse-cool
parse-hic	parse-hic
parse-hicpro	parse-hicpro
reexports	reexports
refocus	AllGenerics
refocus,HiCExperiment,character-method	HiCExperiment
regions,HiCExperiment-method	HiCExperiment
resolution	AllGenerics
resolution,ContactsFile-method	ContactsFile-class
resolution,HiCExperiment-method	HiCExperiment
resolutions	AllGenerics
resolutions,HiCExperiment-method	HiCExperiment
scores	AllGenerics
scores,HiCExperiment,character-method	HiCExperiment
scores,HiCExperiment,missing-method	HiCExperiment
scores,HiCExperiment,numeric-method	HiCExperiment
scores,HiCExperiment-method	HiCExperiment
scores<-	AllGenerics
scores<-,HiCExperiment,character,numeric-method	HiCExperiment
scores<-,HiCExperiment-method	HiCExperiment
sdiag	utils
seqinfo,HiCExperiment-method	HiCExperiment
show,AggrHiCExperiment-method	AggrHiCExperiment
show,CoolFile-method	CoolFile-class
show,HiCExperiment-method	HiCExperiment
show,HicFile-method	HicFile-class
show,HicproFile-method	HicproFile-class
slices	AllGenerics
slices,AggrHiCExperiment,character-method	AggrHiCExperiment
slices,AggrHiCExperiment,missing-method	AggrHiCExperiment
slices,AggrHiCExperiment,numeric-method	AggrHiCExperiment
sortPairs	utils
splitCoords	utils
subsetByOverlaps,HiCExperiment,GRanges-method	HiCExperiment
topologicalFeatures	AllGenerics
topologicalFeatures,HiCExperiment,character-method	HiCExperiment
topologicalFeatures,HiCExperiment,missing-method	HiCExperiment
topologicalFeatures,HiCExperiment,numeric-method	HiCExperiment
topologicalFeatures,HiCExperiment-method	HiCExperiment
topologicalFeatures<-	AllGenerics
topologicalFeatures<-,HiCExperiment,character,GRangesOrGInteractions-method	HiCExperiment
topologicalFeatures<-,HiCExperiment-method	HiCExperiment
trans	AllGenerics
trans,HiCExperiment-method	HiCExperiment
zoom	AllGenerics
zoom,HiCExperiment,numeric-method	HiCExperiment
[,HiCExperiment,character,ANY,ANY-method	HiCExperiment
[,HiCExperiment,GInteractions,ANY,ANY-method	HiCExperiment
[,HiCExperiment,logical,ANY,ANY-method	HiCExperiment
[,HiCExperiment,numeric,ANY,ANY-method	HiCExperiment
[,HiCExperiment,Pairs,ANY,ANY-method	HiCExperiment
[,HiCExperiment-method	HiCExperiment
