6d5f4622cb4474f55f0e1081a8a8423e *DESCRIPTION
e23cc265209e0497dfa59ffa1a483252 *NAMESPACE
7133ab5d4929537b42d28377034b2ccf *NEWS
5b64ae254c960d271eb0465692e2e1dd *R/AllClasses.R
be4ca6810caf6a18ec9f25de7d562ead *R/AllGenerics.R
35f4b22878444394cd52584cc8bd33b4 *R/CoverageFunctions.R
bddb19b64f7f47895317e88535880851 *R/Functions.R
d68204264cbe7496984457e145c4cadc *R/PlotFunction.R
b1572861aba888febbbc62c70ff74ee8 *R/bindingsites.R
692ca0e5a57cc63a115b77cd05f46a57 *R/bsfind.R
dca32e65f5a44f25958f11baf2f92fc9 *R/coveragePlots.R
8163e148b3e36e123dd91cf05acbae61 *R/differentialFunctions.R
918fb7fcec6d1b2beef3c4841dc41d37 *R/differentialPlots.R
0043082f2fae78016ad94ddfef65492c *R/exports.R
f338b45f2ff6c12728b7cd22f166831b *R/helper.R
d1c214b1db00a802ddb2d5ccd03af64c *R/helperPlots.R
8fd13113205099352eda4da7a6b47b51 *R/helperSpecific.R
67e2083e6c5f63a4f71c4a916254f450 *R/methods.R
e9cbe718302fdb4f07b814ad0e053841 *R/workflow.R
fafe8156526757efd0c54e6e4acee14a *README.md
20a9282912c8c95ff025a0f4142423db *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
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99f27fb80fcd7ef42bbfde535207f82d *inst/extdata/rep4_clip_plus.bw
1625d9cd90264007171b13e302e78586 *inst/script/PrepareExampleData.R
ea9306ee911334d2ca46eef5295a3e07 *inst/script/PrepareTestBsfSet.R
2f764b4a97eaa77864dfe103f3f9e52a *man/BSFDataSet.Rd
90c0098ae76245f85c0b472fc1b40090 *man/BSFind.Rd
e9197bb8725a225ce6d863b5b3b7fb9d *man/add-BSFDataSet.Rd
ed9343a2f5f80ccd5be9d8cf93e4833f *man/annotateWithScore.Rd
1557a48ea2e48fa240a4de984ec66a95 *man/assignToGenes.Rd
814f6e1238e57d1d833f76898ff2cf9d *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
7a5649fc0462c17836bc80a5297c9b41 *man/pureClipGeneWiseFilter.Rd
5e433cd9eb13906951a3b56090c1f301 *man/pureClipGlobalFilter.Rd
5fab762d805dd4348d49ccbb328cea44 *man/pureClipGlobalFilterPlot.Rd
3d4b622acc3e0a2c57ec2f1369d7ab63 *man/quickFigure.Rd
0c3134b0d20830b8e106dd9a50c23638 *man/rangeCoveragePlot.Rd
821a4a1633c131bcc1e982bc88bc458e *man/reproducibilityCutoffPlot.Rd
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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
5e78bd5609281eea305c2f1f7dd374bb *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
b4a7d8cbdbfd571f507c61324d5758cb *tests/testthat/test_BSFDataSet.R
99fe0ac95fbf145ea155ab320ddf030e *tests/testthat/test_BSFDataSetFromBigWig.R
4a3dacc4c22dfcdaa019a743620fedbb *tests/testthat/test_annotateWithScore.R
90992be24201e7de8ab9aea08f29ab27 *tests/testthat/test_assignToGenes.R
3af889f21faa3f993167a8ecc3a4dfe5 *tests/testthat/test_assignToTranscriptRegions.R
715b8d6a0c24d2e04face73d7cddf224 *tests/testthat/test_bsfind.R
f188780a79b12e261e7c1794e413c82f *tests/testthat/test_calculateBsBackground.R
dea1d88cd64825e0e103483eb1e9b187 *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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b2f0f36aebf652406f621dc2c4a27460 *tests/testthat/test_makeBindingSites.R
a8b3dd3f4b235a4d7ddc8089efe32733 *tests/testthat/test_pureClipGeneWiseFilter.R
19809c36a4ed85b92bab6751f61756c7 *tests/testthat/test_pureClipGlobalFilter.R
bf26c841a370c29811eda77ca70e733e *tests/testthat/test_reproducibilityFilter.R
619135365a0315530f4e5e8412cc2ecb *tests/testthat/test_sampleToCondition.R
36616a01c5e97db33fb13a82a58497d0 *tests/testthat/test_subsetting.R
34748a9a6d9fb26dbd619db346eb4e90 *tests/testthat/test_supportRatio.R
8178cdd15b37541d3fb646faedfafbf8 *tests/testthat/test_targetGeneSpectrumPlot.R
641c7aff63e9e74578ffc00e519740d0 *vignettes/images/background.png
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c3012a3bed419cb15694eed352822b67 *vignettes/my_fig_main.png
db8408cb1525ad0d727a396029f57c02 *vignettes/my_fig_supp.png
dddb10ff326c177c39934983552efa7f *vignettes/references.bib
d549bf40296f9e23d2e2ead8ceb8d96e *vignettes/vignette.Rmd
