Capture Hi-C Analysis Engine
add.covariates
add.fragment.coordinates
bedtools.installed
check.model.identifiability
check.split.data.numerical.fit
chicane
combine.replicates
compare.replicates
convert.bam
convert.hicup.digest.bed
convert.standard.format
convert.to.one.based
create.locus.plot
create.modelfit.plot
distance.bin
distance.split
fill.in.zeros
filter.fragments
fit.glm
fit.model
get.combination.count
get.components
get.distance
get.id.components
get.interaction.id
get.trans.counts
is.glm.nb.maxiter.warning
check.glm.nb.theta.error
is.glm.nb.theta.warning
model.rows.sanity.check
model.try.catch
multiple.testing.correct
prepare.data
read.bed
run.model.fitting
smart.split
stratified.enrichment.sample
test.enrichment
verify.interaction.data
Toolkit for processing and calling interactions in capture Hi-C data. Converts BAM files into counts of reads linking restriction fragments, and identifies pairs of fragments that interact more than expected by chance. Significant interactions are identified by comparing the observed read count to the expected background rate from a count regression model.