Files in chicane
Capture Hi-C Analysis Engine
MD5
NEWS
NAMESPACE
DESCRIPTION
R/read.bed.R
R/is.glm.nb.maxiter.warning.R
R/convert.hicup.digest.bed.R
R/test.enrichment.R
R/fill.in.zeros.R
R/compare.replicates.R
R/bedtools.installed.R
R/distance.bin.R
R/run.model.fitting.R
R/is.glm.nb.theta.error.R
R/get.components.R
R/prepare.data.R
R/model.rows.sanity.check.R
R/add.covariates.R
R/filter.fragments.R
R/verify.interaction.data.R
R/get.id.components.R
R/fit.model.R
R/multiple.testing.correct.R
R/chicane-pkg.R
R/convert.bam.R
R/get.combination.count.R
R/smart.split.R
R/is.glm.nb.theta.warning.R
R/convert.to.one.based.R
R/check.split.data.numerical.fit.R
R/create.modelfit.plot.R
R/distance.split.R
R/get.trans.counts.R
R/stratified.enrichment.sample.R
R/get.distance.R
R/get.interaction.id.R
R/check.model.numerical.fit.R
R/fit.glm.R
R/create.locus.plot.R
R/combine.replicates.R
R/chicane.R
R/bre80.R
R/model.try.catch.R
R/convert.standard.format.R
R/add.fragment.coordinates.R
inst/doc/Getting_Started.Rmd
inst/doc/Visualising_Interactions.html
inst/doc/Getting_Started.R
inst/doc/Getting_Started.html
inst/doc/Visualising_Interactions.Rmd
inst/doc/Visualising_Interactions.R
inst/extdata/Bre80_2q35.bam
inst/extdata/T47D_2q35_filtered_chicane_calls.txt
inst/extdata/read_count_test.bam
inst/extdata/gencode_2q35.gtf
inst/extdata/GRCh38_HindIII_chr2.bed.gz
inst/extdata/HiCUP_digest_example.txt
inst/extdata/T47D_chr2_CTCF.bed.gz
inst/extdata/2q35.bed
inst/extdata/read_count_test_cis.bam
inst/bin/prepare_bam.sh
build/vignette.rds
tests/testthat.R
tests/testthat/test_prepare.data.R
tests/testthat/test_smart.split.R
tests/testthat/test_chicane.R
tests/testthat/test_fit.model.R
tests/testthat/test_get.trans.counts.R
tests/testthat/test_read.bed.R
tests/testthat/test_check.model.numerical.fit.R
tests/testthat/test_model.rows.sanity.check.R
tests/testthat/test_is.glm.nb.theta.warning.R
tests/testthat/test_get.combination.count.R
tests/testthat/test_convert.hicup.digest.bed.R
tests/testthat/test_verify.interaction.data.R
tests/testthat/test_add.covariates.R
tests/testthat/test_fill.in.zeros.R
tests/testthat/test_add.fragment.coordinates.R
tests/testthat/test_get.id.components.R
tests/testthat/test_test.enrichment.R
tests/testthat/test_is.glm.nb.theta.error.R
vignettes/Getting_Started.Rmd
vignettes/bibliography.bib
vignettes/Visualising_Interactions.Rmd
data/bre80.RData
man/create.modelfit.plot.Rd
man/get.distance.Rd
man/add.fragment.coordinates.Rd
man/is.glm.nb.theta.error.Rd
man/compare.replicates.Rd
man/get.components.Rd
man/get.combination.count.Rd
man/run.model.fitting.Rd
man/distance.split.Rd
man/prepare.data.Rd
man/model.try.catch.Rd
man/create.locus.plot.Rd
man/convert.bam.Rd
man/read.bed.Rd
man/stratified.enrichment.sample.Rd
man/verify.interaction.data.Rd
man/chicane.Rd
man/convert.to.one.based.Rd
man/convert.standard.format.Rd
man/bedtools.installed.Rd
man/check.model.numerical.fit.Rd
man/model.rows.sanity.check.Rd
man/fit.glm.Rd
man/fill.in.zeros.Rd
man/bre80.Rd
man/add.covariates.Rd
man/is.glm.nb.maxiter.warning.Rd
man/multiple.testing.correct.Rd
man/test.enrichment.Rd
man/get.id.components.Rd
man/fit.model.Rd
man/distance.bin.Rd
man/get.interaction.id.Rd
man/filter.fragments.Rd
man/combine.replicates.Rd
man/get.trans.counts.Rd
man/is.glm.nb.theta.warning.Rd
man/check.split.data.numerical.fit.Rd
man/smart.split.Rd
man/convert.hicup.digest.bed.Rd
