Files in ZarnackGroup/BindingSiteFinder

Binding site defintion based on iCLIP data

R/AllClasses.R R/AllGenerics.R R/CoverageFunctions.R R/Functions.R R/PlotFunction.R R/bindingsites.R R/bsfind.R R/coveragePlots.R R/differentialFunctions.R R/differentialPlots.R R/exports.R R/helper.R R/helperPlots.R R/helperSpecific.R R/methods.R R/workflow.R README.md inst/script/PrepareExampleData.R inst/script/PrepareTestBsfSet.R man/BSFDataSet.Rd man/BSFind.Rd man/add-BSFDataSet.Rd man/annotateWithScore.Rd man/assignToGenes.Rd man/assignToTranscriptRegions.Rd man/bindingSiteCoveragePlot.Rd man/bindingSiteDefinednessPlot.Rd man/calculateBsBackground.Rd man/calculateBsFoldChange.Rd man/calculateSignalToFlankScore.Rd man/clipCoverage.Rd man/collapseReplicates.Rd man/combineBSF.Rd man/coverageOverRanges.Rd man/duplicatedSitesPlot.Rd man/estimateBsWidth.Rd man/estimateBsWidthPlot.Rd man/exportTargetGenes.Rd man/exportToBED.Rd man/filterBsBackground.Rd man/geneOverlapsPlot.Rd man/getMeta.Rd man/getName.Rd man/getRanges.Rd man/getSignal.Rd man/getSummary.Rd man/globalScorePlot.Rd man/imputeBsDifferencesForTestdata.Rd man/makeBindingSites.Rd man/makeBsSummaryPlot.Rd man/mergeCrosslinkDiagnosticsPlot.Rd man/mergeSummaryPlot.Rd man/plotBsBackgroundFilter.Rd man/plotBsMA.Rd man/plotBsVolcano.Rd man/processingStepsFlowChart.Rd man/processingStepsTable.Rd man/pureClipGeneWiseFilter.Rd man/pureClipGlobalFilter.Rd man/pureClipGlobalFilterPlot.Rd man/quickFigure.Rd man/rangeCoveragePlot.Rd man/reproducibilityCutoffPlot.Rd man/reproducibilityFilter.Rd man/reproducibilityFilterPlot.Rd man/reproducibilitySamplesPlot.Rd man/reproducibilityScatterPlot.Rd man/setMeta.Rd man/setName.Rd man/setRanges.Rd man/setSignal.Rd man/setSummary.Rd man/show.Rd man/subset-BSFDataSet.Rd man/summary.Rd man/supportRatio.Rd man/supportRatioPlot.Rd man/targetGeneSpectrumPlot.Rd man/transcriptRegionOverlapsPlot.Rd man/transcriptRegionSpectrumPlot.Rd tests/testthat.R tests/testthat/test_BSFDataSet.R tests/testthat/test_BSFDataSetFromBigWig.R tests/testthat/test_annotateWithScore.R tests/testthat/test_assignToGenes.R tests/testthat/test_assignToTranscriptRegions.R tests/testthat/test_bsfind.R tests/testthat/test_calculateBsBackground.R tests/testthat/test_calculateBsFoldChange.R tests/testthat/test_collapseSamples.R tests/testthat/test_combine.R tests/testthat/test_coverage.R tests/testthat/test_coverageOverRanges.R tests/testthat/test_estimateBsWidth.R tests/testthat/test_filterBsBackground.R tests/testthat/test_makeBindingSites.R tests/testthat/test_pureClipGeneWiseFilter.R tests/testthat/test_pureClipGlobalFilter.R tests/testthat/test_reproducibilityFilter.R tests/testthat/test_subsetting.R tests/testthat/test_supportRatio.R vignettes/vignette.Rmd