210bd734b915d91b3836376e72c3a2c1 *DESCRIPTION
a9cce65e4bb44c65305da3d4d01bec8c *LICENSE
298a7d3621950b3948ae22afc421caa5 *NAMESPACE
2a9a40d259d805269efac10405d54821 *NEWS
22c0ed4577c95e1df9746f747eb261fd *R/AllGenerics.R
a54537c18ad18933c8fd1a1b8c3ddd7a *R/GRange_method.R
1713f8c18954878fa647dbccfecfb791 *R/annotate.R
b733a8ed8e01635e2e33cb98501041b1 *R/class.R
f33c4b6bb101003be33b814f173d2340 *R/count.R
1db32a62426ae8bc6662a8492515098e *R/data.R
ffe1e6a093b1f86aab257a45450f7bd8 *R/distance.R
1c0ed37c25593936602d8eeeb2f73a1e *R/formatConverter.R
b0f66f974f2b4d6411a78f2cd8815e99 *R/getset.R
70d7f6cecca2726d374b1ddc6e23c6b8 *R/linkSet-package.R
5ba6b1c2bbd846dc09d9e7b95758be3d *R/methods.R
f0b65b967ce5e04854d66c6041c8ba28 *R/statical.R
22a379e5ac5cf04fa11f7a9151240d98 *R/test_helper.R
c142c91b2c4bacbaf56cce78a4fd923a *R/visualization.R
9b002496218e71eeb57c13f9c6505ca0 *README.md
f1fe812d036aba03b4106d30bcca4990 *build/vignette.rds
f1d966bc28de875920d2274b8254f8f7 *data/linkExample.rda
94b684bdafc216464b813d3ebe80c42c *inst/doc/hic_workthrough.R
f7df125752ba5311e524c137b488c44a *inst/doc/hic_workthrough.Rmd
4cde8e706e8d74aca42f742ffeffd924 *inst/doc/hic_workthrough.html
66b81c29948b896162aa064c6811ee9f *inst/doc/linkSet.R
b38e2a6c851a2a89a8548640991946e0 *inst/doc/linkSet.Rmd
f0d2a9652f65d84223b1cbf14c26a4ab *inst/doc/linkSet.html
3202ee0d7d8fe4936241e29db66f11d5 *inst/extdata/Embryo_body.bed.gz
8cdbc7388d8597151f00d673cfbcf23a *inst/extdata/toyExample.pair.gz
1d1fc421cd3480062edc58bfe8eb487b *inst/scripts/generate_embryo.sh
1805aebf9ecf8d3b25c690993f937d73 *inst/scripts/generate_pair.sh
9bd92701ef2da45a1007e4f205ab694e *man/Convert.Rd
2f05af671cfeb74d6fa1caac9870b5f0 *man/Embryo_body.Rd
940eed60fbe30b48ca0d917746ef6395 *man/annotateInter-linkSet-method.Rd
1d43eedb2dcf4dda5751627e7080b573 *man/annotatePromoter-linkSet-method.Rd
a953755787e22aae033368569b0cc9a0 *man/as.GInteractions.Rd
7fd5c049de506dbef935c83f5b6f6408 *man/as.data.frame-linkSet-method.Rd
3fe23c612795cbac5ff974e16e0ca951 *man/baitGInteractions.Rd
bcce141d517f1306298ca324c0f199c4 *man/character_Or_missing-class.Rd
ca324b148153fdb322364b1b9722a8f6 *man/checkPackages.Rd
05512fb231c84b5bfa43822e6f498bca *man/checkSplitDataNumericalFit.Rd
d2cb199b3df3e141a13916b0387cefb1 *man/chicane.Rd
586203035cd5b14d952fa7dca1ec3ad3 *man/cleanUnusedRegions.Rd
15d6cd36e54d74b64a821d3556af4664 *man/convertToGrange.Rd
345d2582abb6d54883afe5f255a9c312 *man/countInteractibility.Rd
3e430cd122afc187a52803f45a12fad2 *man/countInteractions.Rd
a674de81da9bc97da6ec914400514ad9 *man/createSampleLinkSet.Rd
4f5256245af44ce6147cf533d6f9d89e *man/crossGeneEnhancer-linkSet-method.Rd
283c24b8090d2a3c4caa523b5a70db12 *man/diagnoseLinkSet-linkSet-method.Rd
e07594d195295bf6750f2f722e44d70d *man/enforceOrder.Rd
5cd3359bdc26df02e77e5d242f5c9360 *man/exportInterBed.Rd
b92ef934b7a55ad37ca82b05ddef30be *man/exportToLinkSet.Rd
10289e6c12977e08494279b2cbb966b8 *man/exportWashU.Rd
3584bcd3655e762a8ca6ff6643253408 *man/figures/logo.png
3350b4a3ca3d9a4cd3cee40d28a2f895 *man/filterLinks-linkSet-method.Rd
8c46762346d703825c8067277c16d162 *man/geom_linkset.Rd
c05cb104a7fbfe2c3bd4071765d53883 *man/getDistOutput.Rd
2cef5a5db31014f830e6d0fc8673efb7 *man/linkExample.Rd
a8e7e3bdf31f05840bcc04a3c90cce8c *man/linkSet-GRange-Methods.Rd
9b255c66a44382cbe78baa83dc5568e2 *man/linkSet-GRanges-GRanges-character_Or_missing-method.Rd
f29143f9280d0bba5c315600d19b0ff8 *man/linkSet-accessors.Rd
b52ba247cedafd0d09ae9d5ce7615fc3 *man/linkSet-character-GRanges-character_Or_missing-method.Rd
3627315bc583df899a12be30859f9d9a *man/linkSet-class.Rd
9a768863d37143b249d81447f1464ef2 *man/linkSet-package.Rd
6ef8e904521ecbce41a57f02df1b1671 *man/linkSet-subset-methods.Rd
261f189e689479823fa305e37dd6f9b5 *man/linkSet.Rd
1faebd5b1985a9a8d21c6532e5f7b492 *man/oe-set.Rd
27ff9a2cb398bc0d9c04b0b9400eaa99 *man/orderLinks-linkSet-method.Rd
9b898b3310ea90925ddc2765f4954dd0 *man/pairdist-linkSet-method.Rd
11602ab922040fc749458ea2abb9970d *man/pasteAnchor.Rd
156092e6b29df698479d2edd1c21731a *man/plotBaits.Rd
59cdeab41b4a9d037833fd5269168050 *man/plotGenomicRanges-linkSet-method.Rd
8aaf2dcca4bcd329c701a740170709c4 *man/plotGenomicRanges.Rd
1c566e3f605e2bfb4d32d7414ce7a0bd *man/reduceRegions.Rd
3b7b811d4551fef546eea5339c6d89d5 *man/regionsBait-set.Rd
112879e6b45467e9ef7a81bfb0e4f982 *man/run_chicane.Rd
f91c00b589b7f29ccff0e737c652aafa *man/show.Rd
f5417d704079990ed181a7c413ae02b8 *man/showLinkSet.Rd
498c34ee60038453516c3be0131d18d7 *man/themeLinkset.Rd
70e951ab53859878ff8664734b92200f *man/themeRange.Rd
d732f4f3a0a5468f62c8c75114611547 *man/unchecked_anchor1-set.Rd
af2b762e058d7b1f8c6b2c328a6e2971 *man/unchecked_anchor2-set.Rd
2c4bc1dc380685666feed22a5d2e272e *man/withTxDb.Rd
f9bb7d634de66e31e5ddb226d0f30b05 *tests/testthat.R
c663d3485f344560ec7f62009b1b3e71 *tests/testthat/test_annotate.R
e14bd533a9f9638bfddb11f412208935 *tests/testthat/test_convert.R
68997ce663b787b8d19f785b1d4eba83 *tests/testthat/test_count.R
67785a90fd19f375f82b2d50b50b6204 *tests/testthat/test_dist.R
c7d008ec1f554fc4d1646ad485a5d05c *tests/testthat/test_grange.R
57cc20ea05f4055f2b90ef500d2f9f6f *tests/testthat/test_linkSet.R
1145ba0037bc41940dd3ff494776b026 *tests/testthat/test_statistic.R
f7df125752ba5311e524c137b488c44a *vignettes/hic_workthrough.Rmd
4a03a03deb13ea4005d11aa9625ac81e *vignettes/img/9.10_data_structure.png
2cf6530c30ba81a07bfe0c601f8ed469 *vignettes/img/linkSetImport.png
d9df70d31550847b14826cbee42fd577 *vignettes/img/linksetmethod.png
01ddf262a81b060c1b2e464cd1237e25 *vignettes/img/overview.png
b38e2a6c851a2a89a8548640991946e0 *vignettes/linkSet.Rmd
