ChIPseeker for ChIP peak Annotation, Comparison, and
Visualization
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Documentation for package ‘ChIPseeker’ version 1.45.0
Help Pages
| . | . |
| annotatePeak | annotatePeak |
| as.data.frame.csAnno | as.data.frame.csAnno |
| as.GRanges | as.GRanges |
| check_upstream_and_downstream | check upstream and downstream parameter |
| combine_csAnno | combine_csAnno |
| covplot | covplot |
| csAnno-class | Class "csAnno" This class represents the output of ChIPseeker Annotation |
| downloadGEObedFiles | downloadGEObedFiles |
| downloadGSMbedFiles | downloadGSMbedFiles |
| dropAnno | dropAnno |
| enrichAnnoOverlap | enrichAnnoOverlap |
| enrichPeakOverlap | enrichPeakOverlap |
| getAnnoStat | getAnnoStat |
| getBioRegion | getBioRegion |
| getGeneAnno | getGeneAnno |
| getGenomicAnnotation | getGenomicAnnotation |
| getGEOgenomeVersion | getGEOgenomeVersion |
| getGEOInfo | getGEOInfo |
| getGEOspecies | getGEOspecies |
| getNearestFeatureIndicesAndDistances | getNearestFeatureIndicesAndDistances |
| getPromoters | getPromoters |
| getSampleFiles | getSampleFiles |
| getTagMatrix | getTagMatrix |
| getTagMatrix.binning.internal | getTagMatrix.binning.internal |
| getTagMatrix.internal | getTagMatrix.internal |
| getTagMatrix2 | getTagMatrix2 |
| getTagMatrix2.binning.internal | internal function |
| getTagMatrix2.internal | getTagMatrix2.internal |
| gsminfo | Information Datasets |
| info | Information Datasets |
| makeBioRegionFromGranges | makeBioRegionFromGranges |
| overlap | overlap |
| peakHeatmap | peakHeatmap |
| peakHeatmap_multiple_Sets | peakHeatmap |
| peak_Profile_Heatmap | peak_Profile_Heatmap |
| plotAnnoBar | plotAnnoBar method generics |
| plotAnnoBar-method | Class "csAnno" This class represents the output of ChIPseeker Annotation |
| plotAnnoBar-method | plotAnnoBar method generics |
| plotAnnoBar.data.frame | plotAnnoBar.data.frame |
| plotAnnoPie | plotAnnoPie method generics |
| plotAnnoPie-method | Class "csAnno" This class represents the output of ChIPseeker Annotation |
| plotAnnoPie-method | plotAnnoPie method generics |
| plotAnnoPie.csAnno | plotAnnoPie |
| plotAvgProf | plotAvgProf |
| plotAvgProf.binning | plotAvgProf.binning |
| plotAvgProf2 | plotAvgProf |
| plotDistToTSS | plotDistToTSS method generics |
| plotDistToTSS-method | Class "csAnno" This class represents the output of ChIPseeker Annotation |
| plotDistToTSS-method | plotDistToTSS method generics |
| plotDistToTSS.data.frame | plotDistToTSS.data.frame |
| plotMultiProf | internal function for plotPeakProf_MultiWindows |
| plotMultiProf.binning | internal function |
| plotMultiProf.binning.internal | internal function |
| plotMultiProf.normal | internal function |
| plotMultiProf.normal.internal | internal function |
| plotPeakProf | plotPeakProf_MultiWindows |
| plotPeakProf2 | plotPeakProf2 |
| plotPeakProf_MultiWindows | plotPeakProf_MultiWindows |
| readPeakFile | readPeakFile |
| seq2gene | seq2gene |
| show | show method |
| show-method | Class "csAnno" This class represents the output of ChIPseeker Annotation |
| show-method | show method |
| shuffle | shuffle |
| subset-method | Class "csAnno" This class represents the output of ChIPseeker Annotation |
| tagHeatmap | tagHeatmap |
| tagMatrixList | Information Datasets |
| ucsc_release | Information Datasets |
| upsetplot | upsetplot method |
| upsetplot-method | Class "csAnno" This class represents the output of ChIPseeker Annotation |
| vennpie | vennpie method generics |
| vennpie-method | Class "csAnno" This class represents the output of ChIPseeker Annotation |
| vennplot | vennplot |
| vennplot.peakfile | vennplot.peakfile |