Package: BindingSiteFinder 2.3.1
BindingSiteFinder: Binding site defintion based on iCLIP data
Precise knowledge on the binding sites of an RNA-binding protein (RBP) is key to understand (post-) transcriptional regulatory processes. Here we present a workflow that describes how exact binding sites can be defined from iCLIP data. The package provides functions for binding site definition and result visualization. For details please see the vignette.
Authors:
BindingSiteFinder_2.3.1.tar.gz
BindingSiteFinder_2.3.1.zip(r-4.5)BindingSiteFinder_2.3.1.zip(r-4.4)BindingSiteFinder_2.3.1.zip(r-4.3)
BindingSiteFinder_2.3.1.tgz(r-4.4-any)BindingSiteFinder_2.3.1.tgz(r-4.3-any)
BindingSiteFinder_2.3.1.tar.gz(r-4.5-noble)BindingSiteFinder_2.3.1.tar.gz(r-4.4-noble)
BindingSiteFinder_2.3.1.tgz(r-4.4-emscripten)BindingSiteFinder_2.3.1.tgz(r-4.3-emscripten)
BindingSiteFinder.pdf |BindingSiteFinder.html✨
BindingSiteFinder/json (API)
NEWS
# Install 'BindingSiteFinder' in R: |
install.packages('BindingSiteFinder', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/zarnackgroup/bindingsitefinder/issues
On BioConductor:BindingSiteFinder-2.3.1(bioc 3.20)BindingSiteFinder-2.2.0(bioc 3.19)
Last updated 1 months agofrom:b6b8472341
Exports:annotateWithScoreassignToGenesassignToTranscriptRegionsbindingSiteCoveragePlotbindingSiteDefinednessPlotBSFDataSetBSFDataSetFromBigWigBSFindcalculateBsBackgroundcalculateBsFoldChangecalculateSignalToFlankScoreclipCoveragecollapseReplicatescombineBSFcoverageOverRangesduplicatedSitesPlotestimateBsWidthestimateBsWidthPlotexportTargetGenesexportToBEDfilterBsBackgroundgeneOverlapsPlotgetMetagetNamegetRangesgetSignalgetSummaryglobalScorePlotimputeBsDifferencesForTestdatamakeBindingSitesmakeBsSummaryPlotmergeCrosslinkDiagnosticsPlotmergeSummaryPlotplotBsBackgroundFilterplotBsMAplotBsVolcanoprocessingStepsFlowChartprocessingStepsTablepureClipGeneWiseFilterpureClipGlobalFilterpureClipGlobalFilterPlotquickFigurerangeCoveragePlotreproducibilityCutoffPlotreproducibilityFilterreproducibilityFilterPlotreproducibilitySamplesPlotreproducibilityScatterPlotsetMetasetNamesetRangessetSignalsetSummaryshowsummarysupportRatiosupportRatioPlottargetGeneSpectrumPlottranscriptRegionOverlapsPlottranscriptRegionSpectrumPlot
Dependencies:abindAnnotationDbiaskpassbase64encBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobbslibcachemcirclizecliclueclustercodetoolscolorspaceComplexHeatmapcpp11crayoncurlDBIDelayedArraydigestdistributionaldoParalleldplyrevaluatefansifarverfastmapfontawesomeforcatsforeachformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesGetoptLongggdistggforceggplot2GlobalOptionsgluegtablehighrhtmltoolshttrIRangesisobanditeratorsjquerylibjsonlitekableExtraKEGGRESTknitrlabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmenumDerivopensslpillarpkgconfigplogrplyrpngpolyclippurrrquadprogR6rappdirsRColorBrewerRcppRcppEigenRCurlrestfulrRhtslibrjsonrlangrmarkdownRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorssassscalesshapesnowSparseArraystringistringrSummarizedExperimentsvglitesyssystemfontstibbletidyrtidyselecttinytextweenrUCSC.utilsutf8vctrsviridisLitewithrxfunXMLxml2XVectoryamlzlibbioc