Introduction | Data input | Importing sample data | Importing custom data | Summarizing Overlaps of Query Regions with Genomic Annotation Features | Querying the annotation file | Finding targeted gene types | Extending the annotation feature space | Plotting overlap counts between query regions and transcript features | Obtaining a table of overlap counts between query regions and genes | Profiling the coverage of query regions across transcript features | Coverage profile of query regions at feature boundaries | Coverage profile of query regions for all transcript features | Discriminative Motif Discovery | Calculating enriched motifs | motif analysis: getting motif summary statistics | Functional enrichment analysis | Generating a full report | A test run for human | A custom run for human | To turn off certain modules of the report | To run the pipeline for species other than human | To turn off verbose output and progress bars | Printing raw data generated by the runReport function | Acknowledgements

Introduction | Preparing the inputs | Project Data File | GTF File (genome annotations) | Creating a RSQLite database | Generating a meta-analysis report | Acknowledgements