API for YuLab-SMU/ChIPseeker
ChIPseeker for ChIP peak Annotation, Comparison, and Visualization
| Global functions | |
|---|---|
| . | Man page |
| .ChIPseekerEnv | Source code |
| .onAttach | Source code |
| ChIPseeker | Man page |
| ChIPseeker-package | Man page |
| GRangesList | Man page |
| IDType | Source code |
| TXID2EG | Source code |
| TXID2EGID | Source code |
| TXID2TXEG | Source code |
| addGeneAnno | Source code |
| annoPie | Source code |
| annoPie3D | Source code |
| annotatePeak | Man page Source code |
| arrange.GRanges | Source code |
| as.GRanges | Man page Source code |
| as.data.frame.csAnno | Man page Source code |
| batchGetGSMsuppFile | Source code |
| check_upstream_and_downstream | Man page Source code |
| combine_csAnno | Man page Source code |
| covplot | Man page Source code |
| csAnno-class | Man page |
| downloadGEO.internal | Source code |
| downloadGEObedFiles | Man page Source code |
| downloadGSMbedFiles | Man page Source code |
| dropAnno | Man page Source code |
| enrichAnnoOverlap | Man page Source code |
| enrichOverlap.peak.internal | Source code |
| enrichPeakOverlap | Man page Source code |
| filter.GRanges | Source code |
| generate_break_lbs | Source code |
| generate_colors | Source code |
| getAllFlankingGene | Source code |
| getAnnoStat | Man page Source code |
| getBioRegion | Man page Source code |
| getChrCov | Source code |
| getCols | Source code |
| getFirstHitIndex | Source code |
| getGEOInfo | Man page Source code |
| getGEOgenomeVersion | Man page Source code |
| getGEOspecies | Man page Source code |
| getGSMsuppFile | Source code |
| getGene | Source code |
| getGeneAnno | Man page Source code |
| getGenomicAnnoStat | Source code |
| getGenomicAnnotation | Man page Source code |
| getGenomicAnnotation.internal | Source code |
| getGenomicVersion | Source code |
| getIntersectLength | Source code |
| getNearestFeatureIndicesAndDistances | Man page Source code |
| getPalette | Source code |
| getPromoters | Man page Source code |
| getSampleFiles | Man page Source code |
| getSgn | Source code |
| getTagCiMatrix | Source code |
| getTagCount | Source code |
| getTagMatrix | Man page Source code |
| getTagMatrix.binning.internal | Man page Source code |
| getTagMatrix.internal | Man page Source code |
| getTagMatrix2 | Man page Source code |
| getTagMatrix2.binning.internal | Man page Source code |
| getTagMatrix2.internal | Man page Source code |
| get_exonList | Source code |
| get_gsminfo | Source code |
| get_intronList | Source code |
| gsminfo | Man page |
| info | Man page |
| is.dir | Source code |
| isBedFile | Source code |
| isPeakFeatureOverlap | Source code |
| is_valid_color | Source code |
| is_valid_palette | Source code |
| list_to_dataframe | Source code |
| loadPeak | Source code |
| loadTxDb | Source code |
| makeBioRegionFromGranges | Man page Source code |
| make_label | Source code |
| merge_two_si | Source code |
| mutate.GRanges | Source code |
| overlap | Man page Source code |
| parseBootCiPerc | Source code |
| parse_targetPeak_Param | Source code |
| peak2DF | Source code |
| peakDF2GRanges | Source code |
| peakHeatmap | Man page |
| peakHeatmap_multiple_Sets | Man page |
| peak_Profile_Heatmap | Man page |
| plotAnnoBar | Man page |
| plotAnnoBar,csAnno,ANY-method | Man page |
| plotAnnoBar,csAnno-method | Man page |
| plotAnnoBar,list-method | Man page |
| plotAnnoBar.data.frame | Man page Source code |
| plotAnnoPie | Man page |
| plotAnnoPie,csAnno,ANY-method | Man page |
| plotAnnoPie,csAnno-method | Man page |
| plotAnnoPie.csAnno | Man page Source code |
| plotAvgProf | Man page Source code |
| plotAvgProf.binning | Man page |
| plotAvgProf.internal | Source code |
| plotAvgProf2 | Man page |
| plotDistToTSS | Man page |
| plotDistToTSS,csAnno,ANY-method | Man page |
| plotDistToTSS,csAnno-method | Man page |
| plotDistToTSS,list-method | Man page |
| plotDistToTSS.data.frame | Man page Source code |
| plotMultiProf | Man page |
| plotMultiProf.binning | Man page |
| plotMultiProf.binning.internal | Man page |
| plotMultiProf.normal | Man page |
| plotMultiProf.normal.internal | Man page |
| plotPeakProf | Man page Source code |
| plotPeakProf2 | Man page |
| plotPeakProf_MultiWindows | Man page |
| prepareGSMInfo | Source code |
| readPeakFile | Man page Source code |
| reexports | Man page |
| rel | Man page |
| rename.GRanges | Source code |
| seq2gene | Man page Source code |
| show | Man page |
| show,csAnno,ANY-method | Man page |
| show,csAnno-method | Man page |
| shuffle | Man page Source code |
| sortChrName | Source code |
| subset,csAnno-method | Man page |
| subset.csAnno | Source code |
| tagHeatmap | Man page |
| tagMatrixList | Man page |
| ucsc_release | Man page |
| updateGenomicAnnotation | Source code |
| upsetplot | Man page |
| upsetplot,csAnno-method | Man page |
| upsetplot.csAnno | Source code |
| vennpie | Man page |
| vennpie,csAnno-method | Man page |
| vennpie.csAnno | Source code |
| vennplot | Man page Source code |
| vennplot.peakfile | Man page Source code |
