Man pages for luslab/hiclipr
Analyses hiCLIP data

AlignReadsBowtieAlign and merge reads using Bowtie (as in original paper,...
AnnotateHybridAnnotate hybrid data.table
AnnotateHybridArmAnnotate GRanges arm
ConvertToDataTableConvert GRanges to data.table
ConvertToGenomicCoordinatesConvert to genomic coordinates
ConvertToGRangesConvert data.table to GRanges
CreateBEDCreate BED file
CreateBowtieIndicesCreate Bowtie indices
CreateDirectoriesCreate directory structure
CreateNonRedundantHybridsCreate non-redundant set of hybrids
DemultiplexReadsDemultiplex reads using experimental barcode
EvaluateBarcodesEvaluate Barcodes
ExportBEDExport BED file
ExtractHybridsRemove adapters to select hybrid reads
ExtractRandomBarcodesExtract random barcodes and leave experiment barcode at front
FindDuplexFind Duplex starts
FindDuplexPositionsFind Duplex starts
FindIslandsFind confident islands
FindNonIslandHybridsFind non-island hybrid reads
GetSequenceGet sequence
LoadBAMLoads hybrid BAM file
PlotGenicRegionPlot genic region
PlotHybridRegionPlot hybrid source
PlotIntraInterRatioPlot intra-inter ratio (for genic reads)
PlotLoopLengthPlot loop length
PlotRegionMatePlot region mate
RunRNAHybridRun RNA hybrid
SelectGenicHybridSelect genic reads
luslab/hiclipr documentation built on May 21, 2017, 3:44 p.m.