add.covariates          add.covariates
add.fragment.coordinates
                        add.fragment.coordinates
bedtools.installed      bedtools.installed
bre80                   Bre80 Cell Line
check.model.numerical.fit
                        check.model.identifiability
check.split.data.numerical.fit
                        check.split.data.numerical.fit
chicane                 chicane
combine.replicates      combine.replicates
compare.replicates      compare.replicates
convert.bam             convert.bam
convert.hicup.digest.bed
                        convert.hicup.digest.bed
convert.standard.format
                        convert.standard.format
convert.to.one.based    convert.to.one.based
create.locus.plot       create.locus.plot
create.modelfit.plot    create.modelfit.plot
distance.bin            distance.bin
distance.split          distance.split
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.components          get.components
get.distance            get.distance
get.id.components       get.id.components
get.interaction.id      get.interaction.id
get.trans.counts        get.trans.counts
is.glm.nb.maxiter.warning
                        is.glm.nb.maxiter.warning
is.glm.nb.theta.error   check.glm.nb.theta.error
is.glm.nb.theta.warning
                        is.glm.nb.theta.warning
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
