Calculate, visualize and analyse overlap between genomic regions
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Documentation for package ‘OGRE’ version 1.8.0
Help Pages
| OGRE-package | OGRE package to calculate, analyze and visiualize overlap between annotated genomic region datasets |
| addDataSetFromHub | Add dataSet from AnnotationHub |
| addGRanges | Add GenomicRanges |
| covPlot | Coverage plot |
| extendGRanges | Extend a GRanges object |
| extractPromoters | Extract promoter |
| fOverlaps | Find overlaps |
| gvizPlot | Generate Gviz plot |
| listPredefinedDataSets | List predefined datasets |
| loadAnnotations | Load annotation datasets |
| makeExampleGRanges | Make an example GRanges dataset |
| makeExampleOGREDataSet | Make a example OGRE dataset |
| OGREDataSet | BuildOGREDataSet |
| OGREDataSetFromDir | BuildOGREDataSetFromDir |
| plotHist | Plot histogram |
| readDataSetFromFolder | Read dataset(s) from folder |
| SHREC | SHREC SHiny interface for REgion Comparison |
| subsetGRanges | Subset a GRanges object |
| summarizeOverlap | Calculates min/max/average overlap |
| sumPlot | Generate summary plot |