1c2bdc501aaf6d4aaef910836bd433cb *DESCRIPTION
2e6bf6cb2532adcaa2cd9f4392d0dccd *NAMESPACE
4accf0b02500edc736e1a0b52ab286cf *NEWS
986a2e9edcbab4526f2176a94d797751 *R/AllClasses.R
be4ca6810caf6a18ec9f25de7d562ead *R/AllGenerics.R
35f4b22878444394cd52584cc8bd33b4 *R/CoverageFunctions.R
93a66dd3b9220e6316fa5e74dda4d0cf *R/Functions.R
de3bf9896189334378d3d2f2282ed56b *R/PlotFunction.R
b1572861aba888febbbc62c70ff74ee8 *R/bindingsites.R
692ca0e5a57cc63a115b77cd05f46a57 *R/bsfind.R
dca32e65f5a44f25958f11baf2f92fc9 *R/coveragePlots.R
b19b0e361fecdf778303bfd0ffc34baf *R/differentialFunctions.R
79ea7c64292860c6e2476a3f4e26b043 *R/differentialPlots.R
0043082f2fae78016ad94ddfef65492c *R/exports.R
f338b45f2ff6c12728b7cd22f166831b *R/helper.R
d1c214b1db00a802ddb2d5ccd03af64c *R/helperPlots.R
acd6b19b9126c568f35cb9acbafcd499 *R/helperSpecific.R
ca1069a629d859d215a028ab1bdde8a9 *R/methods.R
081443968ee7c85a98eeafebfdc4316d *R/workflow.R
15075343e0aaf433a501944730d68c83 *README.md
e2d7bcb461a04eb1acc5d38158bece3e *build/vignette.rds
cbfffca6b4b6628c87b61f4f3a391160 *inst/CITATION
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03397defa0d98fd976f092ab04b2746f *inst/extdata/PureCLIP_crosslink_sites_examples.bed
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c2c5db42f7513ae55e0074ff546d6a95 *inst/extdata/regions.rds
bc67a111eada44e67ef2e2e3670936c9 *inst/extdata/rep1_clip_minus.bw
cb43026a8d14c4b351860ae2a3f42420 *inst/extdata/rep1_clip_plus.bw
024721d8147af35dcffd3a50e88a15b5 *inst/extdata/rep2_clip_minus.bw
91769e9ade7daac74a1615416d5c1d5e *inst/extdata/rep2_clip_plus.bw
4c9afc10b932af691252715721e941f6 *inst/extdata/rep3_clip_minus.bw
e6126ae1bba1c8d7d1ed8fa0fc793bdb *inst/extdata/rep3_clip_plus.bw
f3dee0f0d4285411f2b3ef42d3b48929 *inst/extdata/rep4_clip_minus.bw
99f27fb80fcd7ef42bbfde535207f82d *inst/extdata/rep4_clip_plus.bw
b453e2b61b7a7781778679dc495b4d08 *inst/script/PrepareExampleData.R
ea9306ee911334d2ca46eef5295a3e07 *inst/script/PrepareTestBsfSet.R
c02d6bcd29318e4c84ba3768197386a3 *man/BSFDataSet.Rd
90c0098ae76245f85c0b472fc1b40090 *man/BSFind.Rd
e9197bb8725a225ce6d863b5b3b7fb9d *man/add-BSFDataSet.Rd
ed9343a2f5f80ccd5be9d8cf93e4833f *man/annotateWithScore.Rd
c30eecc85eaa8291641296efea6d6941 *man/assignToGenes.Rd
b2a4aa2d6053cf311c0579a875fcdbe0 *man/assignToTranscriptRegions.Rd
eb79d9caf8c6164595b36208193e41a9 *man/bindingSiteCoveragePlot.Rd
7655b5571e9909f0c2a1d04c2c3cbd40 *man/bindingSiteDefinednessPlot.Rd
3762ff99fcf764d1aeee7b79e790e656 *man/calculateBsBackground.Rd
023fbaa1dceb65e9ecb7b8a9dc82505d *man/calculateBsFoldChange.Rd
91985f1cf06b5b37cb188e420886d885 *man/calculateSignalToFlankScore.Rd
e28574682e585b81a06b5466cd9c762c *man/clipCoverage.Rd
2640a1299ba290b7b638b9e7d59e6ea5 *man/collapseReplicates.Rd
c5272c51ac06a7fce5dd7a3f9169e6f2 *man/combineBSF.Rd
a1abcc38fca5a701bac25b91bc793c07 *man/coverageOverRanges.Rd
e604b7b41bee27787cb86542250ad811 *man/duplicatedSitesPlot.Rd
5f6f7262ca4c64d78a8d8274592ceb75 *man/estimateBsWidth.Rd
7ddaa15cf0cbecc39475acf93c8e01e4 *man/estimateBsWidthPlot.Rd
51baa2c5dddc79e9acd16db860325b8b *man/exportTargetGenes.Rd
8a70093b7b75fd9ec647d6ab5099c496 *man/exportToBED.Rd
460d2f5838f18e0f7360742bc5bc4e05 *man/filterBsBackground.Rd
eeb0517840e7198e513c24e0d202691a *man/geneOverlapsPlot.Rd
5cfc6a1ede7f2171904ca94da4113c21 *man/geneRegulationPlot.Rd
3f177d67dcb6d9bfb45268b3db82ce6e *man/getMeta.Rd
ae75c9514a941311eb27a352a6f20cf0 *man/getName.Rd
c37dcad1cc61c5b01aadeff54acd83b3 *man/getRanges.Rd
37bc434f3a47968bb746f7327deb3a3a *man/getSignal.Rd
9ae415e48c94c7105a03d07d826e3e1a *man/getSummary.Rd
9f82daeed350006e4a0bbe11f7047f21 *man/globalScorePlot.Rd
e6b18cb3ec51d1126917445b34042cd4 *man/imputeBsDifferencesForTestdata.Rd
af5c8283b65b2d27617e5386febc2a53 *man/makeBindingSites.Rd
8d77c46c62453d84c7004f3ac0332f6f *man/makeBsSummaryPlot.Rd
d7d57c09e5fc0d860158c969edf3625a *man/mergeCrosslinkDiagnosticsPlot.Rd
c019dc4d52a8102731d681a283910e26 *man/mergeSummaryPlot.Rd
ac8dc9ae1833079c7847425cf9fb3712 *man/plotBsBackgroundFilter.Rd
b42079bcfd8ecceebb01c1c043943f67 *man/plotBsMA.Rd
1048cc7973801bb89f03a283f70be6e6 *man/plotBsVolcano.Rd
acbae31e4a4dd1bfe3ee045d579622b4 *man/processingStepsFlowChart.Rd
0ed60214a227fa35c22b0b065fbe6c0f *man/processingStepsTable.Rd
248bab5f5a1d8077702448ddc766e600 *man/pureClipGeneWiseFilter.Rd
5e433cd9eb13906951a3b56090c1f301 *man/pureClipGlobalFilter.Rd
5fab762d805dd4348d49ccbb328cea44 *man/pureClipGlobalFilterPlot.Rd
3d4b622acc3e0a2c57ec2f1369d7ab63 *man/quickFigure.Rd
0c3134b0d20830b8e106dd9a50c23638 *man/rangeCoveragePlot.Rd
821a4a1633c131bcc1e982bc88bc458e *man/reproducibilityCutoffPlot.Rd
e45c9658a80ace4d769a8a408ea2b73f *man/reproducibilityFilter.Rd
bd77677cfc208658413aeda416f3de76 *man/reproducibilityFilterPlot.Rd
9b3ece6141dc983634f16f0b218c7f5e *man/reproducibilitySamplesPlot.Rd
7f31d80708306f9055350965ec8f64a8 *man/reproducibilityScatterPlot.Rd
3447f908fd7bf2b70182248d7e012615 *man/setMeta.Rd
a5e91f3b519f82191c358490c23f79a2 *man/setName.Rd
65f471dada48319d1d04b768eded6a73 *man/setRanges.Rd
1f8a61b67d8dbf1965efc21b7501bfcd *man/setSignal.Rd
bf22d42f92ea16174c476ee53c58301b *man/setSummary.Rd
3e5f3ebd638f4f3a7abd313a6dd6f143 *man/show.Rd
474b07164ea1fe7259afb7b8c7c09338 *man/subset-BSFDataSet.Rd
8b23bc5016b51c14c58049dce0075598 *man/summary.Rd
5e4b906c21598c657768cf1e83821be0 *man/supportRatio.Rd
8c9169b9fc5794765d7b4789791b1e06 *man/supportRatioPlot.Rd
90f3676df905d0a8a1df98a3a8e7b26f *man/targetGeneSpectrumPlot.Rd
9a81f95ac8b53eeff49bb9d571c8386e *man/transcriptRegionOverlapsPlot.Rd
052fd19f1391db907bda00147473ecf7 *man/transcriptRegionSpectrumPlot.Rd
513bbebd2a84dcc5436cc87e9e447a75 *tests/testthat.R
dd31c07a578517c90708a626e9a7c2fa *tests/testthat/test.rda
c7a7d173c1ee65236c374cc89bb2382c *tests/testthat/test_BSFDataSet.R
99fe0ac95fbf145ea155ab320ddf030e *tests/testthat/test_BSFDataSetFromBigWig.R
4a3dacc4c22dfcdaa019a743620fedbb *tests/testthat/test_annotateWithScore.R
90992be24201e7de8ab9aea08f29ab27 *tests/testthat/test_assignToGenes.R
8d6a117b4f003cff9ce2c63e103d44be *tests/testthat/test_assignToTranscriptRegions.R
715b8d6a0c24d2e04face73d7cddf224 *tests/testthat/test_bsfind.R
305840abb494f677241d9b29d4a88e68 *tests/testthat/test_calculateBsBackground.R
01d7851e4add152cc66fe7800e8abf6c *tests/testthat/test_calculateBsFoldChange.R
9a4cd2dcba38c3a63c23855221c7c811 *tests/testthat/test_collapseSamples.R
1c4133f289e30ef8548b6e2238ba02fb *tests/testthat/test_combine.R
5b81893a7df2aa7d8464a8e32943cc73 *tests/testthat/test_coverage.R
7bbd11aa03c7767f61b6bbeb66261038 *tests/testthat/test_coverageOverRanges.R
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7a18ea8de7fb1f74e479070215f2e27a *tests/testthat/test_filterBsBackground.R
b2f0f36aebf652406f621dc2c4a27460 *tests/testthat/test_makeBindingSites.R
a8b3dd3f4b235a4d7ddc8089efe32733 *tests/testthat/test_pureClipGeneWiseFilter.R
19809c36a4ed85b92bab6751f61756c7 *tests/testthat/test_pureClipGlobalFilter.R
98d342f62b00f65d1e984a893ccf3330 *tests/testthat/test_reproducibilityFilter.R
36616a01c5e97db33fb13a82a58497d0 *tests/testthat/test_subsetting.R
34748a9a6d9fb26dbd619db346eb4e90 *tests/testthat/test_supportRatio.R
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c3012a3bed419cb15694eed352822b67 *vignettes/my_fig_main.png
db8408cb1525ad0d727a396029f57c02 *vignettes/my_fig_supp.png
dddb10ff326c177c39934983552efa7f *vignettes/references.bib
178b7707a7a2efe5f5491228c3be3010 *vignettes/vignette.Rmd
