d34172c2ae747b75f2f2b4c2c351739f *DESCRIPTION
4760b8cea42bdf9e2bd0ee4e5ffa14b2 *NAMESPACE
93cfbcf63974f524105299ef4a86b2a5 *NEWS
7ba7302aff9bc05429c604f44d53ccaa *R/add.covariates.R
e141b54fdd60761cab361879a3a8622e *R/add.fragment.coordinates.R
6a1695d418ea4f7d421e23b4fa1e79d8 *R/bedtools.installed.R
1f7ee93e66ca073118d74f824097cafa *R/bre80.R
7e591ac338a57b2aff4b11adb705fbef *R/check.model.numerical.fit.R
ae945e4b0ba2dbf234eb778f22a98a32 *R/check.split.data.numerical.fit.R
b4051a680f988a0392db2a9f97a205e7 *R/chicane-pkg.R
c617036da54a54b65682b05f64d0ceda *R/chicane.R
5c4a6bd17c7063f33f926ac1dccc6817 *R/combine.replicates.R
7a4e68cba3dec350340291ec81aacfb5 *R/compare.replicates.R
33819fefb190916a00ddea1c67e4d4c7 *R/convert.bam.R
87f82d85bcf9d45345c1f8a594cc4a31 *R/convert.hicup.digest.bed.R
796133fcf1cedd261a60ff3a6b663832 *R/convert.standard.format.R
676afba2772c4bae60f97a78861eaeb8 *R/convert.to.one.based.R
c3992c1e628cb49e4f0078d27fcfce6c *R/create.locus.plot.R
31f3cdf1583493484d01655e69607551 *R/create.modelfit.plot.R
250ae5f95e123075eb471af96d06f84f *R/distance.bin.R
0783ec85e870e4f6661189ea8942fcaf *R/distance.split.R
a1ab215890673ff061510273b4e3b4a4 *R/fill.in.zeros.R
abddb642a664441df31d73605db567c6 *R/filter.fragments.R
831d1f0d7f24010bac34aac65599a67a *R/fit.glm.R
d3b92a206ee8848d9f522304dc222ca8 *R/fit.model.R
4850814df55da191fb7954074df9f5ed *R/get.combination.count.R
d14a01e2d5f9bb165820c165a7ebf1e8 *R/get.components.R
08e857014c879ec52c32f6364b029558 *R/get.distance.R
55b636b3303c94d9c0f7381c98caaa50 *R/get.id.components.R
14d8e97f79dcec7c95d3738d02e3f28f *R/get.interaction.id.R
2ffaf4dc8236badcd0696116e15b3193 *R/get.trans.counts.R
df292c60fdf080443990a157e4295916 *R/is.glm.nb.maxiter.warning.R
b5da0b8024d80e605a78f14e22dfb017 *R/is.glm.nb.theta.error.R
23da64b799f4410730c80de545931c51 *R/is.glm.nb.theta.warning.R
c12b2d1bfbc5d326df730961a8ed3213 *R/model.rows.sanity.check.R
0b2b0bb53b9180c1bdd3191eda4ecd7d *R/model.try.catch.R
c9b5be792911f3d915ac0254db0fd75a *R/multiple.testing.correct.R
1e363af32ad3b68e63da95ed9b30f851 *R/prepare.data.R
0ad6091b18a7ba50f7d247fbed75d20b *R/read.bed.R
c16fd080f724f80668f904dc018c322f *R/run.model.fitting.R
bebec770c45504212ba57ca7522d6624 *R/smart.split.R
ccd73f636bbfa07f208140eb367dc3bb *R/stratified.enrichment.sample.R
d9f4d32650c1ae239871c2e1f277df39 *R/test.enrichment.R
c747a30c3cb78dcf2b5bd82a48e110de *R/verify.interaction.data.R
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f3c68b5f083dda85ec5addc8f3e53fd0 *data/bre80.RData
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515585c33dedb19a8f1f7c748ebef7e3 *inst/doc/Getting_Started.Rmd
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2e0b49081a1b12fb2fe254cedf1635ab *inst/doc/Visualising_Interactions.html
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8e0324f0ea4ef14fc866fdc9d6617c0c *inst/extdata/Bre80_2q35.bam
77de0629d4337e8589101295e928d2b0 *inst/extdata/GRCh38_HindIII_chr2.bed.gz
4669a4755d16f56edef27d94e2c48369 *inst/extdata/HiCUP_digest_example.txt
08ac28976f25554458f20b220d99902d *inst/extdata/T47D_2q35_filtered_chicane_calls.txt
2f808b14e72d467223a8e5cd6b134458 *inst/extdata/T47D_chr2_CTCF.bed.gz
da9476d831a0e737b7db65ed4153a0ec *inst/extdata/gencode_2q35.gtf
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06e7e9ddf38045653625d5e85f9666aa *inst/extdata/read_count_test_cis.bam
ef9a646517578cc4a5ab50d097ded27c *man/add.covariates.Rd
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e3acbf2aa90202f4f70063612b6b0066 *man/check.split.data.numerical.fit.Rd
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af221d87a08953cd817ad85f3e239d02 *man/combine.replicates.Rd
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3115d0c7b68c9f95aa85e068eb61ae80 *man/create.modelfit.plot.Rd
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0fcdae44a8a26ee9e83b9c2593962309 *man/distance.split.Rd
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d156a655712bb47ff0e8e8ff710ff446 *man/filter.fragments.Rd
437d198ab2f52de770c48957233849a6 *man/fit.glm.Rd
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5e3eb1fdcb43ba7aea21c4559aa57306 *man/get.combination.count.Rd
d17e8b5d0225b854f35013fd776f77ee *man/get.components.Rd
8c05df4358b6aeb2411469c4a8c98ba3 *man/get.distance.Rd
e1469d3ba6d8ee02cbf1379bf6187c8e *man/get.id.components.Rd
73a9ce01cf05f7a160196d74bca2d02c *man/get.interaction.id.Rd
6d4c0038f982d23f68d7932f0b4e716a *man/get.trans.counts.Rd
c83a3c4d67f92002ee8600f20d33bdb2 *man/is.glm.nb.maxiter.warning.Rd
f08ed89f80e515364c36a18e4b1a3e3f *man/is.glm.nb.theta.error.Rd
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4281b37bbb6c665672b59855475c5d73 *man/model.rows.sanity.check.Rd
abae86042e72ebf13b32ad7ffb45fa30 *man/model.try.catch.Rd
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67f6d2ecc8b9acc6ce6a8f157ab96a10 *man/prepare.data.Rd
a4f887482b3789031fc1b50e2e27b5e8 *man/read.bed.Rd
b870c2aa185b55700dbf8b650fcf28f5 *man/run.model.fitting.Rd
973bd5c375ba9c41daadd7f6c2dab38c *man/smart.split.Rd
bfa43c29071642019b4c954ed3091f39 *man/stratified.enrichment.sample.Rd
a093721504ef3d0942dbeefbda15d203 *man/test.enrichment.Rd
249d2cf76429e8f3f52303d60752a307 *man/verify.interaction.data.Rd
dff64dc16cbb6a9b9d804baa91887674 *tests/testthat.R
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fa9dcd27131f769efad88365591de6f3 *tests/testthat/test_prepare.data.R
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34c63410a52ee8719cb106f714ce32fb *tests/testthat/test_smart.split.R
dfaa597ab4e515a47238a735dbdf5875 *tests/testthat/test_test.enrichment.R
7ffffa975fd2fa765b26e3ccc0ad6200 *tests/testthat/test_verify.interaction.data.R
515585c33dedb19a8f1f7c748ebef7e3 *vignettes/Getting_Started.Rmd
43a62fba28efa85b10aa6dcc17827b09 *vignettes/Visualising_Interactions.Rmd
3328e02afd7ccfd6597a4f30cb225587 *vignettes/bibliography.bib
