Files in ZarnackGroup/BindingSiteFinder
Binding site defintion based on iCLIP data
.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
NEWS
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/CITATION
inst/extdata/PureCLIP_crosslink_sites_examples.bed
inst/extdata/bds.rda
inst/extdata/bsf_icon.png
inst/extdata/gns.rds
inst/extdata/regions.rds
inst/extdata/rep1_clip_minus.bw
inst/extdata/rep1_clip_plus.bw
inst/extdata/rep2_clip_minus.bw
inst/extdata/rep2_clip_plus.bw
inst/extdata/rep3_clip_minus.bw
inst/extdata/rep3_clip_plus.bw
inst/extdata/rep4_clip_minus.bw
inst/extdata/rep4_clip_plus.bw
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.rda
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/images/background.png
vignettes/images/bsf_promotion.png
vignettes/images/model.png
vignettes/images/preprocessing.png
vignettes/my_fig_main.png
vignettes/my_fig_supp.png
vignettes/references.bib
vignettes/vignette.Rmd
