Preface | Motivation | Prerequisites | Installation | Quick start | A quick look at the input data | A quick way to define binding sites | The quick picture, two figures for the lazy one | Standard workflow | Manage the input data | Build the BSFDataSet | Construct the annotation objects | Create annotation for genes | Create annotation for transcript regions | Performing the main analysis | Deciding on the binding site width | Pre-filtering of crosslink sites | Selection of the binding site width | Apply the gene-wise filter | Merge crosslink sites into binding sites | How to ensure reproducibility among replicates | The replicate-specific threshold | How many replicates are enough? | Do my replicate corrlate well? | Genomic target identification | Target gene identification | Transcript region identification | Assessing further binding site properties | Binding site strength | Binding site definedness | Exporting your results | For additional analysis in R/Bioconductor | Export as UCSC BED | Export genes and feature lists | Export iCLIP signal | Diagnostic coverage polots | Visualize the iCLIP coverage | Trace back a binding site | Gene wise coverage | Variations of the standard workflow | Normalize transcript regions | How to manually test different binding site sizes | If you already know your binding site size | Call utility functions seperately | Construct your own pipeline | Work without a gene annotation | Reproducibility scatter before and after correction | Use a different set of transcript regions | Additional functions | Subset data for faster iterations | Merge replicate signal | Exporting iCLIP signal | Calculate coverage | Differential binding analysis | Concept and idea | Preparation of the input data | Define binding sites for each condition | Merge binding sites into a single object for testing | Count matrix generation | Calculate binding sites and background counts | Filter binding site and background counts | Perform differential testing | Display differential results on gene level | Differential binding variations | Starting from scratch | Starting from existing binding sites | How to deal with multiple comparisons? | Using the blacklist regions | Session info | Bibliography