add.covariates	add.covariates
add.fragment.coordinates	add.fragment.coordinates
bedtools.installed	bedtools.installed
bre80	bre80
check.model.numerical.fit	check.model.numerical.fit
check.split.data.numerical.fit	check.split.data.numerical.fit
chicane	chicane
combine.replicates	combine.replicates
convert.bam	convert.bam
convert.hicup.digest.bed	convert.hicup.digest.bed
distance.bin	distance.bin
distance.split	distance.split
fill.in.zeroes	fill.in.zeros
fill.in.zeros	fill.in.zeros
filter.fragments	filter.fragments
fit.glm	fit.glm
fit.model	fit.model
get.combination.count	get.combination.count
get.distance	get.distance
get.id.components	get.id.components
get.trans.counts	get.trans.counts
is.glm.nb.maxiter.warning	is.glm.nb.maxiter.warning
is.glm.nb.theta.error	is.glm.nb.theta.error
is.glm.nb.theta.warning	is.glm.nb.theta.warning
make.modelfit.plot	make.modelfit.plot
model.rows.sanity.check	model.rows.sanity.check
model.try.catch	model.try.catch
multiple.testing.correct	multiple.testing.correct
prepare.data	prepare.data
read.bed	read.bed
run.model.fitting	run.model.fitting
smart.split	smart.split
stratified.enrichment.sample	stratified.enrichment.sample
test.enrichment	test.enrichment
verify.interaction.data	verify.interaction.data
