# Capture Hi-C Analysis Engine

## Documentation for package ‘chicane’ version 0.1.8

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS

## Help Pages

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.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.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