47abb3483db8b92a366dd94a70fffdbe *DESCRIPTION
cb1554ea5a11c101a80adad21a488108 *LICENSE
070896a28a9640d166bd9d710f0bf69c *NAMESPACE
9580ba6f68606838a97e48ded311d70d *NEWS
56f2a74b7a8cd1e9417636acb6b326eb *R/GenotypeBreaks.R
e58c00907ddfe0dff233c1bb65522edf *R/breakSeekr.R
3617e7e219984b9298f517a9bd9f5594 *R/breakpointR-package.R
1f157ea184c66eb59205d46235575b02 *R/breakpointr.R
13d910ed63833d4b7a9b99eb3c8e7142 *R/confidenceInterval.R
72582e323e3eb1a033d0b395de636165 *R/createCompositeFile.R
f24d9d89e7e2013baa88bf73d70d22e8 *R/deltaWCalculator.R
b67f0f602a83251ce1334b9a1c10d464 *R/documented_objects.R
478b365c4f0a0f7b4f24d27fbf3fb72e *R/exportRegions.R
f392490500eb7c25824bc396bb124974 *R/exportUCSC.R
d10557bc88674351bff0fd1c938bab90 *R/global.R
aa863c35a3f3a36c49ba072dac9e54ce *R/hotspotter.R
8f2adb3ed0bc0b3c84daf37675a0b5a5 *R/importReads.R
65807c8c7aa5ab0c5a9acd8b60cbbae4 *R/loadFromFiles.R
7354f8916cf02e7db354f711f16810cb *R/plotting.R
9c1b03553742bf0eb706d3c29f734820 *R/runBreakpointr.R
fe49ba5fff255a3bc876af1ae5c3a22d *R/rwConfig.R
c78483c17524f8955a9dd1280a7e0f20 *R/summarizeBreaks.R
7722ed42f0b306541cd7293ae784c6ef *R/syncReads.R
ae9de9911f834b49fdf071dd288994f6 *R/timedMessage.R
f9f8f5887cbd2edb76e83794c702f650 *R/utils.R
a6a5403ad57c4f355a9367747ffe1c75 *README.md
13d0c35c1e0b9215669d003cff69ee33 *breakpointR_logo.png
78cd228ccef32b71626c8f2111f7d734 *build/vignette.rds
e0f6d883de3fc1d9fcceaa20cf9e157e *inst/doc/breakpointR.R
2cd20b9d735055deb96d4966d203a46e *inst/doc/breakpointR.Rnw
f1079081202f3f2c02d3d37763b0b1a3 *inst/doc/breakpointR.pdf
ccc29eb5a1add551bb21f192c0bfff1a *man/BreakPoint.Rd
5d339930fa87a8af8859637b21d93240 *man/breakSeekr.Rd
ffb7f4f140fe4bb66f31744212f76ef2 *man/breakpointR-package.Rd
45cbe24c1d2d9b3dd27cea72fc087dbd *man/breakpointr.Rd
f208a819bef22934b213b659dcdfc2da *man/breakpointr2UCSC.Rd
65fc3666fba2b2f37051bc550207f5b6 *man/collapseBins.Rd
649fdcfa2633fded704c9d19b2886949 *man/confidenceInterval.Rd
21c258bba3cdd080ed04d96e5a4e5359 *man/confidenceInterval.binomial.Rd
cd7bed4be9afc7fc18a3f38d47489383 *man/createCompositeFile.Rd
b3a439505fc3c4014185b1ef43f163e6 *man/deltaWCalculator.Rd
bfbb9e2034fde04d1a824ca1cf764a28 *man/deltaWCalculatorVariousWindows.Rd
8372aa4a140a1d5aecaef867382669f4 *man/exportRegions.Rd
4228a7af031f81949cb374950c935c92 *man/genotype.binom.Rd
6626375c29378752b06dec3adc1982f5 *man/genotype.fisher.Rd
e6e479c66bd8d3ab4ab83a07a830c6a3 *man/genotyping.Rd
c98153d26217858bdaba523fc1f24469 *man/hotspotter.Rd
7436c262d452ac75ef7db932349f4bda *man/insertchr.Rd
9fb34503e1f9a3039d71661dcbc10c31 *man/loadFromFiles.Rd
9d3909eb201f7693bdd2fb3ed3bffdd6 *man/plotBreakpoints.Rd
6bfb02f09adbd0150fd6199f26eeb509 *man/plotBreakpointsPerChr.Rd
bdd0a8c8f8c1160f8c7c1bd7dee486b4 *man/plotHeatmap.Rd
b33fb20e995d7f06b7ae6a88b17d2388 *man/ranges2UCSC.Rd
687dd49dbf3d2aec696e36cb6e320613 *man/readBamFileAsGRanges.Rd
8ad9e120155147eea5823f25ba7494d1 *man/readConfig.Rd
a1f365ecce8718e48505bcbe6480f1f6 *man/removeDoubleSCEs.Rd
7d9fb65b30ffb6c0d290d50bf91d1a4d *man/removeReadPileupSpikes.Rd
d60dd4c14d46ee138eb9f689f66dda93 *man/runBreakpointr.Rd
5b1ce47e1120dee3f06866b342aa6b60 *man/summarizeBreaks.Rd
64cd28fc326e55ea059cd2203c7f1322 *man/synchronizeReadDir.Rd
ec8affd6f436f7c2cd12ebd4965b2a33 *man/transCoord.Rd
b0071ad7435980b1091b57a06c225b38 *man/writeConfig.Rd
e4163a631051edd1c64c356114beb04e *tests/testthat.R
bfcdd5514a328d2d34004642056a9ea3 *tests/testthat/nobreaks_exampleFile.RData
2583972306e6ca15c23311a9005c6b11 *tests/testthat/test_breakNum.R
9bf753787fde28f76a82a928c10bff71 *tests/testthat/withbreaks_exampleFile.RData
2cd20b9d735055deb96d4966d203a46e *vignettes/breakpointR.Rnw
