cobindR-package	cobindr-package
cobindr-package	cobindr-package
bg_binding_sites	bg_binding_sites
bg_binding_sites,cobindr-method	bg_binding_sites
bg_binding_sites<-	bg_binding_sites
bg_binding_sites<-,cobindr,data.frame-method	bg_binding_sites
bg_pairs	bg_pairs
bg_pairs,cobindr-method	bg_pairs
bg_pairs<-	bg_pairs
bg_pairs<-,cobindr,data.frame-method	bg_pairs
bg_sequences	bg_sequences
bg_sequences,cobindr-method	bg_sequences
bg_sequences<-	bg_sequences
bg_sequences<-,cobindr,list-method	bg_sequences
bg_sequence_origin	bg_sequence_origin
bg_sequence_origin,configuration-method	bg_sequence_origin
bg_sequence_origin<-	bg_sequence_origin
bg_sequence_origin<-,configuration,character-method	bg_sequence_origin
bg_sequence_source	bg_sequence_source
bg_sequence_source,configuration-method	bg_sequence_source
bg_sequence_source<-	bg_sequence_source
bg_sequence_source<-,configuration,character-method	bg_sequence_source
bg_sequence_type	bg_sequence_type
bg_sequence_type,configuration-method	bg_sequence_type
bg_sequence_type<-	bg_sequence_type
bg_sequence_type<-,configuration,character-method	bg_sequence_type
binding_sites	binding_sites
binding_sites,cobindr-method	binding_sites
binding_sites<-	binding_sites
binding_sites<-,cobindr,data.frame-method	binding_sites
cobindR	cobindr-package
cobindr	cobindr-package
cobindr-class	cobindr-class
cobindRConfiguration	cobindRConfiguration
cobindRConfiguration,character-method	cobindRConfiguration
cobindRConfiguration-method	cobindRConfiguration
comment	comment
comment,SeqObj-method	comment
comment<-	comment
comment<-,SeqObj,character-method	comment
compare.samples	cobindr-internal
configuration	configuration
configuration,cobindr-method	configuration
configuration-class	configuration-class
configuration<-	configuration
configuration<-,cobindr,configuration-method	configuration
cpg.content	cobindr-internal
cpg.gc.content	cobindr-internal
determine.cores.option	cobindr-internal
detrending	cobindr-internal
detrending,cobindr-method	cobindr-class
downstream	downstream
downstream,configuration-method	downstream
downstream<-	downstream
downstream<-,configuration,numeric-method	downstream
experiment_description	experiment_description
experiment_description,cobindr-method	experiment_description
experiment_description,configuration-method	experiment_description
experiment_description<-	experiment_description
experiment_description<-,cobindr,character-method	experiment_description
experiment_description<-,configuration,character-method	experiment_description
fdrThreshold	fdrThreshold
fdrThreshold,configuration-method	fdrThreshold
fdrThreshold<-	fdrThreshold
fdrThreshold<-,configuration,numeric-method	fdrThreshold
find.hits	cobindr-internal
find.pairs	find.pairs
find.pairs,cobindr-method	cobindr-class
find.pairs_intern	cobindr-internal
gc.content	cobindr-internal
generate.background	cobindr-internal
generate.background,cobindr-method	cobindr-class
get.bindingsite.ranges	get.bindingsite.ranges
get.bindingsite.ranges,cobindr-method	cobindr-class
get.pairs	get.pairs
get.pairs,cobindr-method	get.pairs
get.pairs-method	get.pairs
get.positions	cobindr-internal
get.significant.pairs	get.significant.pairs
get.significant.pairs,cobindr-method	get.significant.pairs
get.significant.pairs-method	get.significant.pairs
global.permutation	cobindr-internal
id	id
id,configuration-method	id
id<-	id
id<-,configuration,character-method	id
initialize,cobindr-method	cobindr-class
initialize,configuration-method	configuration-class
initialize,SeqObj-method	SeqObj-class
input.pfm.similarity	cobindr-internal
input.pwm	cobindr-internal
input.pwm,cobindr-method	cobindr-class
kl.dist	cobindr-internal
lcm.vector	cobindr-internal
local.permutation	cobindr-internal
location	location
location,SeqObj-method	location
location<-	location
location<-,SeqObj,character-method	location
make.character	cobindr-internal
mart	mart
mart,configuration-method	mart
mart<-	mart
mart<-,configuration,character-method	mart
max_distance	max_distance
max_distance,configuration-method	max_distance
max_distance<-	max_distance
max_distance<-,configuration,numeric-method	max_distance
name	name
name,cobindr-method	name
name,SeqObj-method	name
name<-	name
name<-,cobindr,character-method	name
name<-,SeqObj,character-method	name
normalize.matrix.colSum	cobindr-internal
pairs	pairs
pairs,cobindr-method	pairs
pairs,configuration-method	pairs
pairs<-	pairs
pairs<-,cobindr,data.frame-method	pairs
pairs<-,configuration,character-method	pairs
pairs_of_interest	pairs_of_interest
pairs_of_interest,cobindr-method	pairs_of_interest
pairs_of_interest<-	pairs_of_interest
pairs_of_interest<-,cobindr,factor-method	pairs_of_interest
parallelize	cobindr-internal
path	path
path,configuration-method	path
path<-	path
path<-,configuration,character-method	path
pfm	pfm
pfm,cobindr-method	pfm
pfm.similarity	cobindr-internal
pfm2pwm	cobindr-internal
pfm<-	pfm
pfm<-,cobindr,list-method	pfm
pfm_path	pfm_path
pfm_path,configuration-method	pfm_path
pfm_path<-	pfm_path
pfm_path<-,configuration,character-method	pfm_path
plot.detrending	plot.detrending
plot.detrending,cobindr-method	plot.detrending
plot.detrending-method	plot.detrending
plot.gc	plot.gc
plot.gc,cobindr-method	plot.gc
plot.gc-method	plot.gc
plot.pairdistance	plot.pairdistance
plot.pairdistance,cobindr-method	plot.pairdistance
plot.pairdistance-method	plot.pairdistance
plot.pairdistribution	plot.pairdistribution
plot.pairdistribution,cobindr-method	plot.pairdistribution
plot.pairdistribution-method	plot.pairdistribution
plot.positionprofile	plot.positionprofile
plot.positionprofile,cobindr-method	plot.positionprofile
plot.positionprofile-method	plot.positionprofile
plot.positions	plot.positions
plot.positions,cobindr-method	plot.positions
plot.positions-method	plot.positions
plot.positions.simple	plot.positions.simple
plot.positions.simple,cobindr-method	plot.positions.simple
plot.positions.simple-method	plot.positions.simple
plot.tfbs.heatmap	plot.tfbs.heatmap
plot.tfbs.heatmap,cobindr-method	plot.tfbs.heatmap
plot.tfbs.heatmap-method	plot.tfbs.heatmap
plot.tfbs.venndiagram	plot.tfbs.venndiagram
plot.tfbs.venndiagram,cobindr-method	plot.tfbs.venndiagram
plot.tfbs.venndiagram-method	plot.tfbs.venndiagram
plot.tfbslogo	plot.tfbslogo
plot.tfbslogo,cobindr-method	plot.tfbslogo
plot.tfbslogo-method	plot.tfbslogo
predicted2pwm	predicted2pwm
predicted2pwm,cobindr-method	predicted2pwm
predicted2pwm-method	predicted2pwm
pseudocount	pseudocount
pseudocount,configuration-method	pseudocount
pseudocount<-	pseudocount
pseudocount<-,configuration,character-method	pseudocount
pValue	pValue
pValue,configuration-method	pValue
pValue<-	pValue
pValue<-,configuration,numeric-method	pValue
query.motifDb	cobindr-internal
read.background.fasta	cobindr-internal
read.background.fasta,configuration-method	configuration-class
read.pfm	cobindr-internal
read.pfm,configuration-method	configuration-class
read.sequences	cobindr-internal
read.sequences,configuration-method	configuration-class
read.transfac.pfm	cobindr-internal
removeSpecialCharacters	cobindr-internal
rtfbs	rtfbs
rtfbs,cobindr-method	rtfbs
rtfbs-method	rtfbs
rtfbs.intern	cobindr-internal
rtfbs.intern,SeqObj-method	SeqObj-class
search.gadem	search.gadem
search.gadem,cobindr-method	search.gadem
search.gadem-method	search.gadem
search.pwm	search.pwm
search.pwm,cobindr-method	search.pwm
search.pwm-method	search.pwm
seqObj	seqObj
seqObj,DNAString,character,character,character,character,character-method	seqObj
SeqObj-class	SeqObj-class
seqObj-method	seqObj
sequence	sequence
sequence,SeqObj-method	sequence
sequence<-	sequence
sequence<-,SeqObj,DNAString-method	sequence
sequences	sequences
sequences,cobindr-method	sequences
sequences<-	sequences
sequences<-,cobindr,list-method	sequences
sequence_origin	sequence_origin
sequence_origin,configuration-method	sequence_origin
sequence_origin<-	sequence_origin
sequence_origin<-,configuration,character-method	sequence_origin
sequence_source	sequence_source
sequence_source,configuration-method	sequence_source
sequence_source<-	sequence_source
sequence_source<-,configuration,character-method	sequence_source
sequence_type	sequence_type
sequence_type,configuration-method	sequence_type
sequence_type<-	sequence_type
sequence_type<-,configuration,character-method	sequence_type
species	species
species,configuration-method	species
species,SeqObj-method	species
species<-	species
species<-,configuration-method	species
species<-,SeqObj-method	species
testCpG	testCpG
testCpG,cobindr-method	testCpG
testCpG-method	testCpG
threshold	threshold
threshold,configuration-method	threshold
threshold<-	threshold
threshold<-,configuration,numeric-method	threshold
uid	uid
uid,cobindr-method	uid
uid,SeqObj-method	uid
uid<-	uid
uid<-,cobindr,character-method	uid
uid<-,SeqObj,character-method	uid
uniqueFilename	cobindr-internal
upstream	upstream
upstream,configuration-method	upstream
upstream<-	upstream
upstream<-,configuration,numeric-method	upstream
wind.cpg.content	cobindr-internal
wind.cpg.gc.content	cobindr-internal
wind.gc.content	cobindr-internal
write,cobindr,character-method	cobindr-class
write,configuration,character-method	configuration-class
write.bindingsites	write.bindingsites
write.bindingsites,cobindr-method	write.bindingsites
write.bindingsites-method	write.bindingsites
write.bindingsites.table	write.bindingsites.table
write.bindingsites.table,cobindr-method	write.bindingsites.table
write.bindingsites.table-method	write.bindingsites.table
write.fasta,SeqObj-method	SeqObj-class
write.pairs	write.pairs
write.pairs,cobindr-method	write.pairs
write.pairs-method	write.pairs
write.sequences	write.sequences
write.sequences,cobindr-method	write.sequences
write.sequences-method	write.sequences
writeDetrending_intern	cobindr-internal
