Capture Hi-C Analysis Engine


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Documentation for package ‘chicane’ version 0.1.4

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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