Man pages for luslab/hiclipr
Analyses hiCLIP data
| AlignReadsBowtie | Align and merge reads using Bowtie (as in original paper,... |
| AnnotateHybrid | Annotate hybrid data.table |
| AnnotateHybridArm | Annotate GRanges arm |
| ConvertToDataTable | Convert GRanges to data.table |
| ConvertToGenomicCoordinates | Convert to genomic coordinates |
| ConvertToGRanges | Convert data.table to GRanges |
| CreateBED | Create BED file |
| CreateBowtieIndices | Create Bowtie indices |
| CreateDirectories | Create directory structure |
| CreateNonRedundantHybrids | Create non-redundant set of hybrids |
| DemultiplexReads | Demultiplex reads using experimental barcode |
| EvaluateBarcodes | Evaluate Barcodes |
| ExportBED | Export BED file |
| ExtractHybrids | Remove adapters to select hybrid reads |
| ExtractRandomBarcodes | Extract random barcodes and leave experiment barcode at front |
| FindDuplex | Find Duplex starts |
| FindDuplexPositions | Find Duplex starts |
| FindIslands | Find confident islands |
| FindNonIslandHybrids | Find non-island hybrid reads |
| GetSequence | Get sequence |
| LoadBAM | Loads hybrid BAM file |
| PlotGenicRegion | Plot genic region |
| PlotHybridRegion | Plot hybrid source |
| PlotIntraInterRatio | Plot intra-inter ratio (for genic reads) |
| PlotLoopLength | Plot loop length |
| PlotRegionMate | Plot region mate |
| RunRNAHybrid | Run RNA hybrid |
| SelectGenicHybrid | Select genic reads |
