Installation | Introduction | Relationship to other motif tools | Workflow overview | The background model | Obtaining a precomputed background | Preparing promoter sequences for pscan() | Scanning from a list of transcripts | Selecting promoters from a gene list | Configuring parallel execution | Data provenance | Session information

Installation | Introduction | The data | The background | From genes to promoters | A small executable scan | Running the scan | Checking the result against a second gene set | Comparison with the published figure | Inspecting the result object | Motif score patterns across promoters | Positional distribution of motif matches | Analysing a motif-selected promoter subset | Summary | Appendix: Comparison with the published analysis | Data provenance | Session information

Installation | Introduction | The data | The background | From genes to promoters | A small executable scan | Running the scan | Inspecting the result object | Motif score patterns across promoters | Positional distribution of motif matches | Analysing a motif-selected promoter subset | Summary | Appendix: Comparison with the published analysis | Data provenance | Session information

Introduction | Installation | Available resources | Retrieval through ExperimentHub | License and provenance | Session information

Introduction | Installation | An executable workflow | Table 1: Motif enrichment analysis and input preparation | Table 2: Background construction | Table 3: Result summaries and visualisation | Data provenance | Session information

Installation | Introduction | A small executable construction and round trip | Part A: Building a standard background | The promoters | The matrices | Building a standard background | Saving and reloading a standard background | Verification against the catalogue | Part B: Building and querying a full background | Saving and reloading a full background | Analysing a foreground by identifier | Part C: Checklist for a new background | Summary | Data provenance | Session information