API for ThomasCarroll/soGGi
Visualise ChIP-seq, MNase-seq and motif occurrence as aggregate plots Summarised Over Grouped Genomic Intervals
| Global functions | |
|---|---|
| $,ChIPprofile-method | Man page |
| ChIPprofile | Man page |
| ChIPprofile-ChIPprofile | Man page |
| ChIPprofile-class | Man page |
| EndRule | Source code |
| GetGRanges | Source code |
| Ops,ChIPprofile,ChIPprofile-method | Man page |
| Ops,ChIPprofile,numeric-method | Man page |
| Ops,numeric,ChIPprofile-method | Man page |
| [[,ChIPprofile,ANY,missing-method | Man page |
| c,ChIPprofile-method | Man page |
| cbind,ChIPprofile-method | Man page |
| chipExampleBig | Man page |
| dropNonPrimary | Source code |
| extractScores | Source code |
| extractSummits | Source code |
| findCovMaxPos | Source code |
| findconsensusRegions | Man page Source code |
| getFragmentLength | Source code |
| getShifts | Source code |
| getSummitScore | Source code |
| groupByOverlaps | Man page Source code |
| ik_Example | Man page |
| ik_Profiles | Man page |
| log,ChIPprofile-method | Man page |
| log2,ChIPprofile-method | Man page |
| makeGRangesWithSummary | Source code |
| makeMotifScoreRle | Man page Source code |
| mean,ChIPprofile-method | Man page |
| motifCov | Source code |
| normalise | Man page |
| normalise,ChIPprofile,character,numeric-method | Man page |
| normalise,ChIPprofile-method | Man page |
| normalise.ChIPprofile | Man page |
| normaliseQuantiles | Man page |
| normaliseQuantiles,ChIPprofile-method | Man page |
| normaliseQuantiles.ChIPprofile | Man page |
| orientBy | Man page Source code |
| plotHeatmap | Source code |
| plotRegion | Man page |
| plotRegion,ChIPprofile-method | Man page |
| plotRegion.ChIPprofile | Man page Source code |
| pwmCov | Man page |
| pwmHitAsCoverage | Source code |
| pwmHitAsGRanges | Source code |
| pwmToCoverage | Man page Source code |
| pwmToGranges | Source code |
| rbind,ChIPprofile-method | Man page |
| regionPlot | Man page Source code |
| rleFromScoresInGRanges | Source code |
| runConsensusRegions | Source code |
| runFindSummit | Source code |
| runGetShifts | Source code |
| runGetSummitScore | Source code |
| runMean | Source code |
| runRegionPlot | Source code |
| singleGRange | Man page |
| soggi | Man page |
| subsetProfile | Source code |
| summitPipeline | Man page Source code |
| winsorizeMatrix | Source code |
| winsorizeVector | Source code |
| zeroToMin | Source code |
| zeroToMin2 | Source code |
