82d1f7d515d5c7278405c93c6c0b75a5 *DESCRIPTION
bcf7d987e195fd2fb31b6c3affc0164c *NAMESPACE
b82c14153fa6e0ecde31fe8fecffabee *NEWS
508b9910bb91c795bc52550d13a3b474 *R/add.covariates.R
e141b54fdd60761cab361879a3a8622e *R/add.fragment.coordinates.R
6a1695d418ea4f7d421e23b4fa1e79d8 *R/bedtools.installed.R
1f7ee93e66ca073118d74f824097cafa *R/bre80.R
a2d1ab62084ca63678c26455c51b7483 *R/check.model.numerical.fit.R
ae945e4b0ba2dbf234eb778f22a98a32 *R/check.split.data.numerical.fit.R
b4051a680f988a0392db2a9f97a205e7 *R/chicane-pkg.R
20db2e4ec9c23af81591184d1b5d9ed1 *R/chicane.R
f33df61721c25e22db3dcd86f5064db8 *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
514af5dd66ddf587cbccebf022b579d7 *R/convert.to.one.based.R
91268acd6626b09e2deae355d787dd39 *R/create.locus.plot.R
9691cece2134acf2fe7d2d284d1c738e *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
cf74d5d98f6b43dfb9358e2e39407e73 *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
5adacd1a7275556a986c5368f0106e8c *R/multiple.testing.correct.R
579f7b01ff251de64f1faecafd322f6f *R/prepare.data.R
c302b63d06b08cc63ecf96bd0196a63a *R/read.bed.R
267833c7e44c7555b4b40ee4e304e898 *R/run.model.fitting.R
bebec770c45504212ba57ca7522d6624 *R/smart.split.R
ccd73f636bbfa07f208140eb367dc3bb *R/stratified.enrichment.sample.R
ef37dd15547daa58187d0eb6dc8fc358 *R/test.enrichment.R
c747a30c3cb78dcf2b5bd82a48e110de *R/verify.interaction.data.R
f6330dff9f8e3bdea525295af30f7e03 *build/vignette.rds
f3c68b5f083dda85ec5addc8f3e53fd0 *data/bre80.RData
6e9d0b3e833252a15bc49e98ec3fbee3 *inst/bin/prepare_bam.sh
66047b2511208c9f56b361551cb5c1d1 *inst/doc/Introduction.R
d1aeed6637aaa75583118a3987ecfa45 *inst/doc/Introduction.Rmd
2956d872301e18a66ade549eef57b03d *inst/doc/Introduction.html
b07509c8de8b480cd9f553108165a1ad *inst/doc/Visualising_Interactions.R
8cb5fa437e4703ab9ee7f9457d5aa72f *inst/doc/Visualising_Interactions.Rmd
ca71bec84c613a9bf949c5855625be05 *inst/doc/Visualising_Interactions.html
9694870bc2e4418cc0da3ff1268baefa *inst/extdata/2q35.bed
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
ee163524629ee726340f7e040152ecf2 *inst/extdata/read_count_test.bam
06e7e9ddf38045653625d5e85f9666aa *inst/extdata/read_count_test_cis.bam
ef9a646517578cc4a5ab50d097ded27c *man/add.covariates.Rd
88484a7e5c2cff2ed34ffbc46ccbda72 *man/add.fragment.coordinates.Rd
0b2a81d5c7b462ae608a1753fb30aed6 *man/bedtools.installed.Rd
98e2d0c02a0f06b5d893e2d40d5f91e1 *man/bre80.Rd
a14a0c006180bc525144d2e096a1220e *man/check.model.numerical.fit.Rd
e3acbf2aa90202f4f70063612b6b0066 *man/check.split.data.numerical.fit.Rd
6adcd72c6f997f258444190ff32cdfae *man/chicane.Rd
fecbae18e2d80d7bbc39f8ffd392ab07 *man/combine.replicates.Rd
80727d579573c100511d1bcfc66d74c7 *man/compare.replicates.Rd
f50f5e3e32e8562fb444d244d0ea283b *man/convert.bam.Rd
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2e08b87ed2e536bc5e024efe9624feff *man/convert.standard.format.Rd
c6e66cf1e75d35e2b934788df567e29b *man/convert.to.one.based.Rd
b9888f01013a10bccadf3179b6e42552 *man/create.locus.plot.Rd
c0dc026fe3c31d88e1754c3a04782e2b *man/create.modelfit.plot.Rd
d246fac775757e9f26a41da743e8191c *man/distance.bin.Rd
0fcdae44a8a26ee9e83b9c2593962309 *man/distance.split.Rd
cfe44209342ee6ecd4101af7029b55c6 *man/fill.in.zeros.Rd
d156a655712bb47ff0e8e8ff710ff446 *man/filter.fragments.Rd
437d198ab2f52de770c48957233849a6 *man/fit.glm.Rd
609c3bc1c2783e90bf9c74b820eac09c *man/fit.model.Rd
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
53c256d95e43da413ff38f2edf7fb584 *man/is.glm.nb.theta.warning.Rd
4281b37bbb6c665672b59855475c5d73 *man/model.rows.sanity.check.Rd
abae86042e72ebf13b32ad7ffb45fa30 *man/model.try.catch.Rd
fbd8598c3a46a2729ab69a8ee6f8c785 *man/multiple.testing.correct.Rd
11450d12585b14e9a1c047559fb602bf *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
2964b41cbbb5cfead6dabf8e83c87920 *man/test.enrichment.Rd
249d2cf76429e8f3f52303d60752a307 *man/verify.interaction.data.Rd
dff64dc16cbb6a9b9d804baa91887674 *tests/testthat.R
05cd966c7c7299fa1427e420a4ce19e8 *tests/testthat/test_add.covariates.R
59ecfd2e80a51518e87e2181a85ecd70 *tests/testthat/test_add.fragment.coordinates.R
890ff622b6f31b7ef0edb49ab9064542 *tests/testthat/test_check.model.numerical.fit.R
642df17a4f29e0b0e4650b8068d81bd4 *tests/testthat/test_chicane.R
03208264f36b3e610f1c899eef263462 *tests/testthat/test_convert.hicup.digest.bed.R
f6f31e06aa74ab53f4d72b025f67002e *tests/testthat/test_fill.in.zeros.R
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8dc3f81c0190955f9048d4e45b54e8db *tests/testthat/test_get.combination.count.R
4e816fbc0ceaf6f820fc7678d0dab2ff *tests/testthat/test_get.id.components.R
f0875bc2cdd7e28341c2a9abe487ba0f *tests/testthat/test_get.trans.counts.R
4c6986cd5ea19020866466e39174ad7c *tests/testthat/test_is.glm.nb.theta.error.R
3fa116b2e58a84597a0f079ef4bca3e4 *tests/testthat/test_is.glm.nb.theta.warning.R
8092eca099aed33c8405b43355dfc608 *tests/testthat/test_model.rows.sanity.check.R
fa9dcd27131f769efad88365591de6f3 *tests/testthat/test_prepare.data.R
e5f4e3e314c0e145ce0d7a262a322afb *tests/testthat/test_read.bed.R
34c63410a52ee8719cb106f714ce32fb *tests/testthat/test_smart.split.R
70d067aee03a3bcf6c5ffe6b7fe4745d *tests/testthat/test_test.enrichment.R
7ffffa975fd2fa765b26e3ccc0ad6200 *tests/testthat/test_verify.interaction.data.R
d1aeed6637aaa75583118a3987ecfa45 *vignettes/Introduction.Rmd
8cb5fa437e4703ab9ee7f9457d5aa72f *vignettes/Visualising_Interactions.Rmd
50456d4636de74b96abd7af08a499a99 *vignettes/bibliography.bib
